Tailored modulation of gene regulation programs via functional enhancer RNA

ABSTRACT

The disclosure provides for eRNA-targeted transcriptional reprogramming through targeted reduction of eRNAs for a clinically relevant gene, TNFSF10, resulting in a selective control of interferon-induced apoptosis. A method of inhibiting a TNFSF10 gene expression in a human cell is disclosed. The methods described herein comprise contacting the human cell with a single-stranded antisense compound consisting of the sequence selected from a set of SEQ ID NOs: disclosed herein, wherein the antisense compound targets an enhancer RNA (eRNA) transcribed from a genomic enhancer sequence or region. The eRNA is an TNFSF10 eRNA sequence comprising the nucleic acid sequence selected from the SEQ ID NOs disclosed herein which inhibits expression of the TNFSF10 gene in the human cell.

PRIORITY CLAIM

This application claims benefit of priority to U.S. Provisional Application Ser. No. 62/924,569, filed Oct. 22, 2019, the entire contents of which are hereby incorporated by reference.

STATEMENT OF GOVERNMENT INTEREST

This invention was made with government support under Grant No. R21 AI107067 and Grant No. R01 CA140485 awarded by the National Institutes of Health. The government has certain rights in the invention.

SEQUENCE LISTING

The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled UTSFP0152US_ST25.txt created Oct. 21, 2020, which is approximately 158 KB in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.

BACKGROUND

Enhancers are key cis-regulatory elements that play an essential role in genome expression to determine cell fates and functions. There are millions of enhancers in the human genome and these enhancers function to shape cell identity by directing distinct genome expression programs. In practice, these enhancers can be systematically identified by the presence of histone modification of H3K4me1 (Heintzman et al., 2009; Heintzman et al., 2007) and H3K27Ac (Rada-Iglesias et al., 2011), the association of transcription factors and coactivators (Heinz et al., 2015), and/or DNase I hypersensitivity (Consortium et al., 2007; Thurman et al., 2012). Functional hierarchies among these enhancers have been described (Ernst and Kellis, 2010). Recently, enhancers were found to be transcriptionally active and generate non-coding RNAs known as enhancer RNAs (eRNAs) as relatively unstable transcripts (Kim et al., 2010; Wang et al., 2011). Several studies have demonstrated eRNA producing enhancers are more potent and associated with higher expression of nearby genes than enhancers without eRNAs. Thus, eRNA producing enhancers are likely active and functional enhancers that define the identity and function of a given cell (Heinz et al., 2015; Romanoski et al., 2015; Wang et al., 2011). Moreover, targeting enhancer activity for therapeutic development has been recently proposed and pursued by several groups and companies (Bradner et al., 2017). By targeting particular enhancers, disease specific modulation of gene expression would be possible without affecting the normal expression in other tissues and organs. However, for the over two million enhancers that have been annotated (Roadmap Epigenomics et al., 2015), currently only tens of thousands of eRNAs have been detected in the human genome through isolated studies (Li et al., 2016). A systematic detection and annotation of eRNAs is necessary to enable functional characterization of eRNA gene regulation, which is a fundamental step toward therapeutic development.

In-depth studies of eRNAs in regulation of key biological processes requires accurate prediction of target genes. Existing methods are mostly based on eRNA and mRNA levels in steady state cells, which may not provide enough information for functional associations. Active enhancers may have multiple nearby genes and vice versa, but functionally associated pairs will be triggered to be transcriptionally active in a synchronized fashion. Thus, eRNA/pre-mRNA dynamics, induced by a stimulus, may represent a highly informative feature for more reliable enhancer target predictions. For example, in the inventor's previous study (Banerjee et al., 2014), the inventor took advantage of the dynamic physical chromatin interactions to identify a functional enhancer responsible for the IFNB1 gene, a critical component of innate and adaptive immunity.

SUMMARY

Active enhancers of the human genome generate long noncoding transcripts known as eRNAs. How dynamic transcriptional changes of eRNAs are physically and functionally linked with target gene transcription remains unclear. To investigate the dynamic functional relationships among eRNAs and target promoters, the inventor obtained a dense time series of GRO-seq and ChIP-seq data to generate a time-resolved enhancer activity map of a cell undergoing an innate antiviral immune response. Dynamic changes in eRNA and pre-mRNA transcription activities suggest distinct regulatory roles of enhancers. Using a criterion based on proximity and transcriptional inducibility, the inventor identified 123 highly confident pairs of virus inducible enhancers and their target genes. These enhancers interact with their target promoters transiently and concurrently at the peak of gene activation. Accordingly, their physical disassociation from the promoters is likely involved in post-induction repression. Functional assessments further establish that these eRNAs are necessary for full induction of the target genes and that a complement of inducible eRNAs functions together to achieve full activation. Lastly, the inventor demonstrates the potential for eRNA-targeted transcriptional reprogramming through targeted reduction of eRNAs for a clinically relevant gene, TNFSF10, resulting in a selective control of interferon-induced apoptosis.

In accordance with the present disclosure, a method of inhibiting a TNFSF10 gene expression in a mammalian cell is disclosed. The method comprises contacting the mammalian cell with a single-stranded antisense compound comprising a sequence selected from a set of SEQ ID NOs: 1, 2, 3, 4, 5, or 6 (shown in the sequence listings in Table 1), wherein the antisense compound targets an enhancer RNA (eRNA) transcribed from a genomic enhancer sequence or region. The eRNA is an TNFSF10 eRNA sequence comprising the nucleic acid sequence selected from SEQ ID NOs: 1, 2, 3, 4, 5, or 6 which inhibits expression of the TNFSF10 gene in the mammalian cell.

In some embodiments, the eRNA transcription is initiated from a RNA polymerase II (PolII) binding site and is capable of elongating bidirectionally. In other embodiments, the eRNA transcription is initiated from a RNA polymerase II (PolII) binding site and is capable of elongating unidirectionally.

It is further conceived, that in some embodiments, the eRNA is capable of enhancing transcription of the TNFSF10 gene. In another aspect of the disclosure, the transcriptional start site of the TNFSF10 gene is located on a chromosome at least about 1 kilobase (kb) from the genomic enhancer sequence or region.

The method may be applied to mammalian cells which may include epithelium cells, a hematopoietic cells, monocytes, macrophages, neurons, breast cells, or cancer cells. In another aspect, the mammalian cell contacted with the antisense compound is in a subject.

The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” The word “about” means plus or minus 5% of the stated number.

It is contemplated that any method or composition described herein can be implemented with respect to any other method or composition described herein. Other objects, features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the disclosure, are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.

BRIEF DESCRIPTION OF THE DRAWINGS

The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present disclosure. The disclosure may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein.

FIGS. 1A-C. Genome-wide eRNA identification. (FIG. 1A) Venn diagram shows the number of all the intergenic transcribed regions (outer circle, light blue), high confident enhancer regions (middle circle, blue), and inducible enhancer regions (inner circle, dark blue). (FIG. 1B) Heatmap summarizes GRO-seq data in eRNA-TSS flanking regions (from 1 Kb upstream to 2 Kb downstream). eRNAs from + (yellow) and − (purple) strands are shown separately. Predicted eRNA-expressing enhancer regions are centered at the TSS. (FIG. 1C) Heatmap (upper panel) and metagene profiles (lower panel) are plotted for epigenetic signals including H3K4me1, H3K27ac and P300 ChIP-seq, DNase-seq, and MNase-seq data.

FIGS. 2A-E. Analysis of differentially expressed genes. (FIG. 2A) Number of up—(red) and down—(blue) regulated genes in time course after virus infection. (FIG. 2B) Number of up—(red) and down—(blue) regulated enhancers through time course. (FIG. 2C) Bar-plot of GO terms enriched for the nearest genes linked to the inducible enhancers. (FIGS. 2D-E) First two principal components of PCA analysis based on mRNA (FIG. 2D) and eRNA (FIG. 2E) expression level. The plots are color-coded with blue representing early and orange late time points.

FIGS. 3A-G. Prediction of virus inducible enhancer-promoter (EP) pairs and validation of their interactions. (FIG. 3A) Heat-map of discordant and concordant expression pairs of target genes (left panel) and their enhancers (right panel). Rows are matched. Expression levels were normalized as log 2 fold-changes relative to 0 h. (FIG. 3B) Diagram describes the identification of inducible enhancers and genes with two indices: the continuity index (CI) and the amplitude index (AI). (FIG. 3C) Number of inducible genes as a function of EP distance is analyzed. Inducible genes were counted within each 100 Kb bin to inducible enhancers (blue points). As a control, the number of all genes in each bin was calculated (grey points). Each group was normalized by the maximum count for the sake of comparison. (FIG. 3D) Enrichment of TF IRF7 motif in the 1 Kb TSS-flanking region of inducible enhancers is shown. (FIG. 3E) Motif enrichment of inducible enhancers. X-axis (absolute enrichment) is the maximum sites per base per peak (SBP). Y-axis (relative enrichment) is the SBP ratio between center (−100 to 100 bp) and rest (−500 to −100 bp and 100 to 500 bp) flanking regions. Point sizes indicate the GRO-seq RPKM fold-changes of TFs. Colors indicate the first time point when the TF reaches half induction. (FIG. 3F) Average PhastCon conservation scores of primates across inducible enhancer regions is shown, relative to randomly selected background. (FIG. 3G) Percentage of inducible human EP pairs that co-exist in other species is shown.

FIGS. 4A-F. Effects of eRNA KD on target genes. (FIG. 4A) Heatmaps of 3C signals for 18 inducible EP pairs and 18 control EP pairs within 200 Kb are shown. Signals are normalized by BAC 3C interaction frequency. (FIG. 4B) Boxplot of 3C log fold-changes is shown (12 h vs. 0 h) for control and induced EP pairs with p-values from Kolmogorov-Smirnov (KS) test. (FIG. 4C) Representative examples of 3C results are shown and compared with GRO-seq signal (RPKM) of the corresponding immune-related genes. (FIG. 4D) Boxplot shows mRNA fold-changes for successful eRNA KD (eRNA <70%) and unsuccessful eRNA KD (eRNA >70%). (FIG. 4E) Heatmap shows mRNA/eRNA log fold-changes. 11 inducible EP pairs and 12 control pairs are included. (FIG. 4F) Representative examples of EP pairs where eRNA KD led to mRNA repression. mRNA/eRNA expression levels were measured by RT-qPCR. Y-axis of expression curves represent GRO-seq signal (RPKM).

FIGS. 5A-C. Effects of multiple enhancers regulation on target gene expression and chromosomal conformation. (FIG. 5A) Schematic diagram of TNFSF10 gene with its multiple enhancers. TNFSF10 has #38 enhancer 27 Kb upstream, and #30 and #5 enhancers 67 Kb and 69 Kb downstream. Colored arrows from the gene and enhancer indicate transcriptional direction. Dashed lines show physical interaction between promoter and enhancer (Interaction A and B) or between different enhancers (Interaction C). (FIG. 5B) Interaction changes between enhancer and promoter regions (Interaction A and B) after individual eRNA KD and all three combined eRNA KD. (FIG. 5C) Three eRNAs (dark blue) and target gene (orange) expression fold changes after each individual eRNA KD and after all three eRNA KD by combining three corresponding siRNAs.

FIGS. 6A-F. Effect of selective inhibition of TNFSF10 by eRNA knockdown on viral induced apoptosis. (FIG. 6A) Simplified representation of the TNFSF10 regulatory network. (FIG. 6B) Relative expression of TNFSF10 in eRNAs knockdown (#5, #30 and #38, triple eRNA KD) and control cells. Triple KD of eRNAs regulating the TNFSF10 results in loss of TNFSF10 expression. (FIG. 6C) Western blot using cleaved caspase-3 antibody to assess apoptosis. Stronger signal of cleaved caspase-3 indicates higher fraction apoptotic cells. As an internal standard, β-actin was used. (FIG. 6D) Cell viability by live cell counts (left panel) and apoptotic cells counts (right panel) for TNFSF10 eRNA and control KD cells are shown. (FIG. 6E) Regulation of apoptosis by TIC10 or virus induced TNFSF10 expression. Possible mechanism through eRNA or direct gene activation is shown in left figure panel. Cell viability by live cell counts (middle panel) for TIC10 treated cell and control cell, and apoptotic cell counts (right panel) for eRNAs KD (triple KD) and control KD in TIC10 treatment for 48 hours. (FIG. 6F) TNFSF10 and its three eRNAs expression fold changes with or without TIC 10 treatment for 48 hours (left panel), and with SeV or TIC10 treatment for 9 hours (right panel).

FIGS. 7A-G. Differentially expressed genes and enhancer by SeV virus infection (FIG. 7A) Histogram of eRNA lengths is shown. X-axis represents the log 10 of eRNA lengths and Y-axis represents the frequency. (FIG. 7B) Gene ontology terms enriched by up-regulated genes (UP) and down-regulated gene (DOWN) are shown with spans of arrows showing duration of gene activation. (FIG. 7C) and (FIG. 7D) Representative genome browser track views of activated immune-related genes, MX1, ISG15 and CCL5, and activated enhancers. Epigenetic (DNase HS, H3K4me1 or H3K4me3 and H3K27ac) signals were normalized to the maximum levels in the regions. The y-axis of GRO-seq data represents normalized read density in reads per 10 million. (FIG. 7E) and (FIG. 7F) The results from t-distributed stochastic neighbor embedding (t-SNE) dimension-reduction analysis for mRNA and eRNA are shown. The plots are color-coded with blue and orange representing early and late time points, respectively. (FIG. 7G) K27Ac enrichment level at the inducible enhancer with time course after virus infection is shown.

FIGS. 8A-B. L2, IFNB1 enhancer and IFNB1 transcriptional changes before (0 h) and after virus infection (9 h). (FIG. 8A) Genome browser track of L2 and IFNB1 is shown. Epigenetic (Sg1, H3K4me1/3 and H3K27ac) signals were normalized by the maximum levels in the regions. The Y-axis represents GRO-seq signal in reads per 10 million. (FIG. 8B) Heat map summarizes GRO-seq RPKM level of L2 and IFNB1 as well as its signal related genes, IRFs, NFκBs, and RELs through the incubation times from 0 hour to 24 hours after infection.

FIGS. 9A-E. Prediction of virus inducible enhancer-promoter (EP) pairs. (FIG. 9A) Average logarithm fold-changes of expressed enhancers near inducible genes, divided into two groups according to EP distance are shown: 0-100 Kb, 100-200 Kb, 200-300 Kb, 300-400 Kb, 400-500 Kb, and 500-600 Kb. (FIG. 9B) Distribution of EP distance between inducible (red) and background (grey) pairs is shown. (FIG. 9C) Average PhastCon conservation scores of each mammal and vertebrate across inducible enhancer regions, relative to randomly selected background are shown. (FIG. 9D) Percentage of inducible human EP pairs (EP distance <500 Kb) that co-exist in other species is shown. (FIG. 9E) Violin plots showing the logarithmic fold change values of enhancers at each time point after infection. Enhancers were divided into groups based on distances from inducible genes.

FIGS. 10A-B. Effects of eRNA KD on target gene transcription. Individual KD experiments of inducible EP pairs are shown. Barplots (FIG. 10A) show the ratio of eRNA (blue)/mRNA (orange) expression level before and after siRNA treatment. Expression profiles (FIG. 10B) show GRO-seq signal (RPKM) of eRNA (blue)/mRNA (orange) during virus incubation time.

FIGS. 11A-C. eRNA KD effect on physical EP interaction. (FIGS. 11A-C) (Top) Schematic diagrams of IFNB1/IF135/MYCBP2 and corresponding enhancer are shown. (Lower left) Fold-change of 3C interaction between EPs after eRNA KD is shown, compared with negative controls.

FIGS. 12A-B Cases of genes with multiple enhancers. (FIGS. 12A-B) Schematic diagram of TLR7 and CD38 and their nearby inducible enhancers is shown (top). Fold changes of eRNA (blue)/mRNA (orange) after individual and combined eRNA KD is plotted.

FIG. 13 . eRNA KD and TIC10 treatment. Y-axis shows the fraction of apoptotic and necrotic cells after 48 h TIC10 incubation, with single, triple or control eRNA KD.

DETAILED DESCRIPTION OF THE EMBODIMENTS

In order to systematically investigate the functionality of eRNAs in the human genome, the inventor employed a battery of comprehensive, unbiased functional genomic experiments across large time points to annotate and investigate huge dynamics of enhancer and target gene activation. He also designed a novel computational strategy for determining functional eRNAs that are virus inducible and mediate innate anti-viral response. Combined with functional assessment using RNAi and time course chromosome conformation capture (3C), the inventor examined functional relevance of these virus inducible eRNAs and their regulatory trajectories and modes of action.

A. eRNAs

Enhancer RNAs (eRNAs) represent a class of relatively short non-coding RNA molecules (50-2000 nucleotides) transcribed from the DNA sequence of enhancer regions. They were first detected in 2010 through the use of genome-wide techniques such as RNA-seq and ChIP-seq. eRNAs can be subdivided into two main classes: 1D eRNAs and 2D eRNAs, which differ primarily in terms of their size, polyadenylation state, and transcriptional directionality. The expression of a given eRNA seems to correlate with the activity of its corresponding enhancer in a context-dependent fashion. Increasing evidence suggests that eRNAs actively play a role in transcriptional regulation in cis and in trans, and while their mechanisms of action remain unclear, a few models have been proposed.

Enhancers as sites of extragenic transcription were initially discovered in genome-wide studies that identified enhancers as common regions of RNA polymerase II (RNA pol II) binding and non-coding RNA transcription. The level of RNA pol II-enhancer interaction and RNA transcript formation were found to be highly variable among these initial studies. Using explicit chromatin signature peaks, a significant proportion (˜70%) of extragenic RNA Pol II transcription start sites were found to overlap enhancer sites in murine macrophages. Out of 12,000 neuronal enhancers in the mouse genome, almost 25% of the sites were found to bind RNA Pol II and generate transcripts. These eRNAs, unlike messenger RNAs (mRNAs), lacked modification by polyadenylation, were generally short and non-coding, and were bidirectionally transcribed. Later studies revealed the transcription of another type of eRNAs, generated through unidirectional transcription, that were longer and contained a poly A tail. Furthermore, eRNA levels were correlated with mRNA levels of nearby genes, suggesting the potential regulatory and functional role of these non-coding enhancer RNA molecules.

eRNAs are transcribed from DNA sequences upstream and downstream of extragenic enhancer regions. Previously, several model enhancers have demonstrated the capability to directly recruit RNA Pol II and general transcription factors and form the pre-initiation complex (PIC) prior to the transcription start site at the promoter of genes. In certain cell types, activated enhancers have demonstrated the ability to both recruit RNA Pol II and also provide a template for active transcription of their local sequences.

Depending on the directionality of transcription, enhancer regions generate two different types of non-coding transcripts, 1D-eRNAs and 2D-eRNAs. The nature of the pre-initiation complex and specific transcription factors recruited to the enhancer may control the type of eRNAs generated. After transcription, the majority of eRNAs remain in the nucleus. In general, eRNAs are very unstable and actively degraded by the nuclear exosome. Not all enhancers are transcribed, with non-transcribed enhancers greatly outnumbering the transcribed ones in the order of magnitude of dozens of thousands in every given cell type.

Evidence that eRNAs cause downstream effects on the efficiency of enhancer activation and gene transcription suggests its functional capabilities and potential importance. The transcription factor p53 has been demonstrated to bind enhancer regions and generate eRNAs in a p53-dependent manner. In cancer, p53 plays a central role in tumor suppression as mutations of the gene are shown to appear in 50% of tumors. These p53-bound enhancer regions (p53BERs) are shown to interact with multiple local and distal gene targets involved in cell proliferation and survival. Furthermore, eRNAs generated by the activation of p53BERs are shown to be required for efficient transcription of the p53 target genes, indicating the likely important regulatory role of eRNAs in tumor suppression and cancer.

Variations in enhancers have been implicated in human disease but a therapeutic approach to manipulate enhancer activity is currently not possible. With the emergence of eRNAs as important components in enhancer activity, powerful therapeutic tools such as RNAi may provide promising routes to target disruption of gene expression.

B. TNFSF10

In the field of cell biology, TNF-related apoptosis-inducing ligand (TRAIL), is a protein functioning as a ligand that induces the process of cell death called apoptosis. TRAIL has also been designated CD253 (cluster of differentiation 253) and TNFSF10 (tumor necrosis factor (ligand) superfamily, member 10).

TRAIL is a cytokine that is produced and secreted by most normal tissue cells. It causes apoptosis primarily in tumor cells, by binding to certain death receptors. TRAIL and its receptors have been used as the targets of several anti-cancer therapeutics since the mid-1990s, such as Mapatumumab. However, as of 2013, these have not shown significant survival benefit. TRAIL has also been implicated as a pathogenic or protective factor in various pulmonary diseases, particularly pulmonary arterial hypertension.

TRAIL shows homology to other members of the tumor necrosis factor superfamily. It is composed of 281 amino acids and has characteristics of a type II transmembrane protein. The N-terminal cytoplasmic domain is not conserved across family members, however, the C-terminal extracellular domain is conserved and can be proteolytically cleaved from the cell surface. TRAIL forms a homotrimer that binds three receptor molecules.

In humans, the gene that encodes TRAIL is located at chromosome 3q26, which is not close to other TNF family members. The genomic structure of the TRAIL gene spans approximately 20 kb and is composed of five exonic segments 222, 138, 42, 106, and 1245 nucleotides and four introns of approximately 8.2, 3.2, 2.3 and 2.3 kb. The TRAIL gene lacks TATA and CAAT boxes and the promoter region contains putative response elements for transcription factors GATA, AP-1, C/EBP, SP-1, OCT-1, AP3, PEA3, CF-1, and ISRE.

TRAIL has been shown to interact with TNFRSF10B. It also binds to the death receptors DR4 (TRAIL-RI) and DR5 (TRAIL-RII). The process of apoptosis is caspase-8-dependent. Caspase-8 activates downstream effector caspases including procaspase-3, −6, and −7, leading to activation of specific kinases. TRAIL also binds the receptors DcR1 and DcR2, which do not contain a cytoplasmic domain (DcR1) or contain a truncated death domain (DcR2). DcR1 functions as a TRAIL-neutralizing decoy-receptor. The cytoplasmic domain of DcR2 is functional and activates NFκB. In cells expressing DcR2, TRAIL binding therefore activates NFκB, leading to transcription of genes known to antagonize the death signaling pathway and/or to promote inflammation. Application of engineered ligands that have variable affinity for different death (DR4 and DR5) and decoy receptors (DCR1 and DCR2) may allow selective targeting of cancer cells by controlling activation of Type 1/Type 2 pathways of cell death and single cell fluctuations.

Luminescent iridium complex-peptide hybrids, which mimic TRAIL, have recently been synthesized in vitro. These artificial TRAIL mimics bind to DR4/DR5 on cancer cells and induce cell death via both apoptosis and necrosis, which makes them a potential candidate for anticancer drug development.

TIC10 (which causes expression of TRAIL) was investigated in mice with various tumor types. The small molecule ONC201 causes expression of TRAIL which kills some cancer cells. In clinical trials only a small proportion of cancer patients responded to various drugs that targeted TRAIL death receptors. Many cancer cell lines develop resistance to TRAIL and limits the efficacy of TRAIL-based therapies.

C. Modified Nucleobases

In certain embodiments, compounds of the disclosure comprise one or more modified nucleosides comprising a modified sugar moiety. Such compounds comprising one or more sugar-modified nucleosides may have desirable properties, such as enhanced nuclease stability or increased binding affinity with a target nucleic acid relative to an oligonucleotide comprising only nucleosides comprising naturally occurring sugar moieties. In certain embodiments, modified sugar moieties are substituted sugar moieties. In certain embodiments, modified sugar moieties are sugar surrogates. Such sugar surrogates may comprise one or more substitutions corresponding to those of substituted sugar moieties.

In certain embodiments, modified sugar moieties are substituted sugar moieties comprising one or more non-bridging sugar substituent, including but not limited to substituents at the 2′ and/or 5′ positions. Examples of sugar substituents suitable for the 2′-position, include, but are not limited to: 2′-F, 2′-OCH₃ (“OMe” or “O-methyl”), and 2′-O(CH₂)₂OCH₃ (“MOE”). In certain embodiments, sugar substituents at the 2′ position is selected from allyl, amino, azido, thio, O-allyl, O—C₁-C₁₀ alkyl, O—C₁-C₁₀ substituted alkyl; OCF₃, O(CH₂)₂SCH₃, O(CH₂)₂—O—N(Rm)(Rn), and O—CH₂—C(═O)—N(Rm)(Rn), where each Rm and Rn is, independently, H or substituted or unsubstituted C₁-C₁₀ alkyl. Examples of sugar substituents at the 5′-position, include, but are not limited to: 5′-methyl (R or S); 5′-vinyl, and 5′-methoxy. In certain embodiments, substituted sugars comprise more than one non-bridging sugar substituent, for example, T-F-5′-methyl sugar moieties (see, e.g., PCT International Application WO 2008/101157, for additional 5′,2′-bis substituted sugar moieties and nucleosides).

Nucleosides comprising 2′-substituted sugar moieties are referred to as 2′-substituted nucleosides. In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from halo, allyl, amino, azido, SH, CN, OCN, CF₃, OCF₃, O, S, or N(R_(m))-alkyl; O, S, or N(R_(m))-alkenyl; O, S or N(R_(m))-alkynyl; O-alkylenyl-O-alkyl, alkynyl, alkaryl, aralkyl, O-alkaryl, O-aralkyl, O(CH₂)₂SCH₃, O(CH₂)₂—O—N(R_(m))(R_(n)) or O—CH₂—C(═O)—N(R_(m))(R_(n)), where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl. These 2′-substituent groups can be further substituted with one or more substituent groups independently selected from hydroxyl, amino, alkoxy, carboxy, benzyl, phenyl, nitro (NO₂), thiol, thioalkoxy (S-alkyl), halogen, alkyl, aryl, alkenyl and alkynyl.

In certain embodiments, a 2′-substituted nucleoside comprises a 2′-substituent group selected from F, NH₂, N₃, OCF₃, O—CH₃, O(CH₂)₃NH₂, CH₂—CH═CH₂, O—CH₂—CH═CH₂, OCH₂CH₂OCH₃, O(CH₂)₂SCH₃, O—(CH₂)₂—O—N(R_(m))(R_(n)), O(CH₂)₂O(CH₂)₂N(CH₃)₂, and N-substituted acetamide (O—CH₂—C(═O)—N(R_(m))(R_(n)) where each R_(m) and R_(n) is, independently, H, an amino protecting group or substituted or unsubstituted C₁-C₁₀ alkyl.

In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, OCF₃, O—CH₃, OCH₂CH₂OCH₃, O(CH₂)₂SCH₃, O(CH₂)₂—O—N(CH₃)₂, —O(CH₂)₂O(CH₂)₂N(CH₃)₂, and O—CH₂—C(═O)—N(H)CH₃.

In certain embodiments, a 2′-substituted nucleoside comprises a sugar moiety comprising a 2′-substituent group selected from F, O—CH₃, and OCH₂CH₂OCH₃.

Certain modified sugar moieties comprise a bridging sugar substituent that forms a second ring resulting in a bicyclic sugar moiety. In certain such embodiments, the bicyclic sugar moiety comprises a bridge between the 4′ and the 2′ furanose ring atoms. Examples of such 4′ to 2′ sugar substituents, include, but are not limited to: —[C(R_(a))(R_(b))]_(n)—, —[C(R_(a))(R_(b))]_(n)—O—, —C(R_(a)R_(b))—N(R)—O— or, —C(R_(a)R_(b))—O—N(R)—; 4′-CH₂-2′, 4′-(CH₂)₂-2′, 4′-(CH₂)—O-2′ (LNA); 4′-(CH₂)—S-2′; 4′-(CH₂)₂-O-2′ (ENA); 4′-CH(CH₃)—O-2′ (cEt) and 4′-CH(CH₂OCH₃)—O-2′, and analogs thereof (see, e.g., U.S. Pat. No. 7,399,845, issued on Jul. 15, 2008); 4′-C(CH₃)(CH₃)—O-2′ and analogs thereof, (see, e.g., WO2009/006478, published Jan. 8, 2009); 4′-CH₂—N(OCH₃)-2′ and analogs thereof (see, e.g., WO2008/150729, published Dec. 11, 2008); 4′-CH₂—O—N(CH₃)-2′ (see, e.g., US2004/0171570, published Sep. 2, 2004); 4′-CH₂—O—N(R)-2′, and 4′-CH₂—N(R)—O-2′-, wherein each R is, independently, H, a protecting group, or C₁-C₁₂ alkyl; 4′-CH₂—N(R)—O-2′, wherein R is H, C₁-C₁₂ alkyl, or a protecting group (see, U.S. Pat. No. 7,427,672, issued on Sep. 23, 2008); 4′-CH₂—C(H)(CH₃)-2′ (see, e.g., Chattopadhyaya et al., J. Org. Chem., 2009, 74, 118-134); and 4′-CH₂—C(═CH₂)-2′ and analogs thereof (see, published PCT International Application WO 2008/154401, published on Dec. 8, 2008).

In certain embodiments, such 4′ to 2′ bridges independently comprise from 1 to 4 linked groups independently selected from —[C(R_(a))(R_(b))]_(n)—, —C(R_(a))═C(R_(b))—, —C(R_(a))═N—, —C(═NR_(a))—, —C(═O)—, —C(═S)—, —O—, —Si(R_(a))₂—, —S(═O)_(x)—, and —N(R_(a))—; wherein:

-   -   x is 0, 1, or 2;     -   n is 1, 2, 3, or 4;     -   each R_(a) and R_(b) is, independently, H, a protecting group,         hydroxyl, C₁-C₁₂ alkyl, substituted C₁-C₁₂ alkyl, C₂-C₁₂         alkenyl, substituted C₂-C₁₂ alkenyl, C₂-C₁₂ alkynyl, substituted         C₂-C₁₂ alkynyl, C₅-C₂₀ aryl, substituted C₅-C₂₀ aryl,         heterocycle radical, substituted heterocycle radical,         heteroaryl, substituted heteroaryl, C₁-C₇ alicyclic radical,         substituted C₅-C₇ alicyclic radical, halogen, OJ₁, NJ₁J₂, SJ₁,         N₃, COOJ₁, acyl (C(═O)—H), substituted acyl, CN, sulfonyl         (S(═O)₂-J₁), or sulfoxyl (S(═O)-J₁); and     -   each J₁ and J₂ is, independently, H, C₁-C₁₂ alkyl, substituted         C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, substituted C₂-C₁₂ alkenyl, C₂-C₁₂         alkynyl, substituted C₂-C₁₂ alkynyl, C₁-C₂ aryl, substituted         C₅-C₂₀ aryl, acyl (C(═O)—H), substituted acyl, a heterocycle         radical, a substituted heterocycle radical, C₁-C₁₂ aminoalkyl,         substituted C₁-C₁₂ aminoalkyl, or a protecting group.

Nucleosides comprising bicyclic sugar moieties are referred to as bicyclic nucleosides or BNAs. Bicyclic nucleosides include, but are not limited to, (A) α-L-Methyleneoxy (4′-CH₂—O-2′) BNA, (B) β-D-Methyleneoxy (4′-CH₂—O-2′) BNA (also referred to as locked nucleic acid or LNA), (C) Ethyleneoxy (4′-(CH₂)₂—O-2′) BNA, (D) Aminooxy (4′-CH₂—O—N(R)-2′) BNA, (E) Oxyamino (4′-CH₂—N(R)—O-2′) BNA, (F) Methyl(methyleneoxy) (4′-CH(CH₃)—O-2′) BNA (also referred to as constrained ethyl or cEt), (G) methylene-thio (4′-CH₂—S-2′) BNA, (H) methylene-amino (4′-CH2-N(R)-2′) BNA, (I) methyl carbocyclic (4′-CH₂—CH(CH₃)-2′) BNA, (J) propylene carbocyclic (4′-(CH₂)₃-2′) BNA, and (K) Methoxy(ethyleneoxy) (4′-CH(CH₂OMe)-O-2′) BNA (also referred to as constrained MOE or cMOE).

Additional bicyclic sugar moieties are known in the art, for example: Singh et al., Chem. Commun., 1998, 4, 455-456; Koshkin et al., Tetrahedron, 1998, 54, 3607-3630; Wahlestedt et al., Proc. Natl. Acad. Sci. U.S.A., 2000,97,5633-5638; Kumar et al., Bioorg. Med. Chem. Lett., 1998, 8, 2219-2222; Singh et al., J. Org. Chem., 1998, 63, 10035-10039; Srivastava et al., J. Am. Chem. Soc., 129(26) 8362-8379 (Jul. 4, 2007); Elayadi et al., Curr. Opinion Invens. Drugs, 2001, 2, 5561; Braasch et al., Chem. Biol., 2001, 8, 1-7; Orum et al., Curr. Opinion Mol. Ther., 2001, 3, 239-243; U.S. Pat. Nos. 7,053,207, 6,268,490, 6,770,748, 6,794,499, 7,034,133, 6,525,191, 6,670,461, and 7,399,845; WO 2004/106356, WO 1994/14226, WO 2005/021570, and WO 2007/134181; U.S. Patent Publication Nos. US2004/0171570, US2007/0287831, and US2008/0039618; U.S. Ser. Nos. 12/129,154, 60/989,574, 61/026,995, 61/026,998, 61/056,564, 61/086,231, 61/097,787, and 61/099,844; and PCT International Applications Nos. PCT/US2008/064591, PCT/US2008/066154, and PCT/US2008/068922.

In certain embodiments, bicyclic sugar moieties and nucleosides incorporating such bicyclic sugar moieties are further defined by isomeric configuration. For example, a nucleoside comprising a 4′-2′ methylene-oxy bridge, may be in the α-L configuration or in the β-D configuration. Previously, α-L-methyleneoxy (4′-CH₂—O-2′) bicyclic nucleosides have been incorporated into antisense oligonucleotides that showed antisense activity (Frieden et al., Nucleic Acids Research, 2003, 21, 6365-6372).

In certain embodiments, substituted sugar moieties comprise one or more non-bridging sugar substituent and one or more bridging sugar substituent (e.g., 5′-substituted and 4′-2′ bridged sugars; PCT International Application WO 2007/134181, published on Nov. 22, 2007, wherein LNA is substituted with, for example, a 5′-methyl or a 5′-vinyl group).

In certain embodiments, modified sugar moieties are sugar surrogates. In certain such embodiments, the oxygen atom of the naturally occurring sugar is substituted, e.g., with a sulfur, carbon or nitrogen atom. In certain such embodiments, such modified sugar moiety also comprises bridging and/or non-bridging substituents as described above. For example, certain sugar surrogates comprise a 4′-sulfur atom and a substitution at the 2′-position (see, e.g., published U.S. Patent Application US20050130923, published on Jun. 16, 2005) and/or the 5′ position. By way of additional example, carbocyclic bicyclic nucleosides having a 4′-2′ bridge have been described (see, e.g., Freier et al., Nucleic Acids Research, 1997, 25(22), 4429-4443 and Albaek et al., J. Org. Chem., 2006, 71, 7731-7740).

In certain embodiments, sugar surrogates comprise rings having other than 5-atoms. For example, in certain embodiments, a sugar surrogate comprises a six-membered tetrahydropyran. Such tetrahydropyrans may be further modified or substituted. Nucleosides comprising such modified tetrahydropyrans include, but are not limited to, hexitol nucleic acid (HNA), anitol nucleic acid (ANA), manitol nucleic acid (MNA) (see Leumann, C J. Bioorg. & Med. Chem. (2002) 10:841-854), and fluoro HNA (F-HNA).

In certain embodiments, the modified THP nucleosides of Formula VII are provided wherein q₁, q₂, q₃, q₄, q₅, q₆ and q₇ are each H. In certain embodiments, at least one of q₁, q₂, q₃, q₄, q₅, q₆ and q₇ is other than H. In certain embodiments, at least one of q₁, q₂, q₃, q₄, q₅, q₆ and q₇ is methyl. In certain embodiments, THP nucleosides of Formula VII are provided wherein one of R₁ and R₂ is F. In certain embodiments, R₁ is fluoro and R₂ is H, R₁ is methoxy and R₂ is H, and R₁ is methoxyethoxy and R₂ is H.

Many other bicyclo and tricyclo sugar surrogate ring systems are also known in the art that can be used to modify nucleosides for incorporation into antisense compounds (see, e.g., review article: Leumann, J. C, Bioorganic & Medicinal Chemistry, 2002, 10, 841-854).

Combinations of modifications are also provided without limitation, such as 2′-F-5′-methyl substituted nucleosides (see PCT International Application WO2008/101157 Published on Aug. 21, 2008 for other disclosed 5′,2′-bis substituted nucleosides) and replacement of the ribosyl ring oxygen atom with S and further substitution at the 2′-position (see U.S. Patent Publication US20050130923, published on Jun. 16, 2005) or alternatively 5′-substitution of a bicyclic nucleic acid (see PCT International Application WO2007/134181, published on Nov. 22, 2007 wherein a 4′-CH₂—O-2′ bicyclic nucleoside is further substituted at the 5′ position with a 5′-methyl or a 5′-vinyl group). The synthesis and preparation of carbocyclic bicyclic nucleosides along with their oligomerization and biochemical studies have also been described (see, e.g., Srivastava et al., J. Am. Chem. Soc. 2007, 129(26), 8362-8379).

In certain embodiments, the present disclosure provides oligonucleotides comprising modified nucleosides. Those modified nucleotides may include modified sugars, modified nucleobases, and/or modified linkages. The specific modifications are selected such that the resulting oligonucleotides possess desirable characteristics. In certain embodiments, oligonucleotides comprise one or more RNA-like nucleosides. In certain embodiments, oligonucleotides comprise one or more DNA-like nucleotides.

In certain embodiments, nucleosides of the present disclosure comprise one or more unmodified nucleobases. In certain embodiments, nucleosides of the present disclosure comprise one or more modified nucleobases.

In certain embodiments, modified nucleobases are selected from: universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil; 5-propynylcytosine; 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl CH₃) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine, 3-deazaguanine and 3-deazaadenine, universal bases, hydrophobic bases, promiscuous bases, size-expanded bases, and fluorinated bases as defined herein. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine ([5,4-b][1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido[5,4-b][1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g., 9-(2-aminoethoxy)-H-pyrimido[5,4-13][1,4]benzoxazin-2(3H)-one), carbazole cytidine (²H-pyrimido[4,5-b]indol-2-one), pyridoindole cytidine (H-pyrido[3′,2′:4,5]pyrrolo[2,3-d]pyrimidin-2-one). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, Kroschwitz, J. I., Ed., John Wiley & Sons, 1990, 858-859; those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613; and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, Crooke, S. T. and Lebleu, B., Eds., CRC Press, 1993, 273-288.

Representative United States Patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include without limitation, U.S. Pat. Nos. 3,687,808; 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121; 5,596,091; 5,614,617; 5,645,985; 5,681,941; 5,750,692; 5,763,588; 5,830,653 and 6,005,096, each of which is herein incorporated by reference in its entirety.

In certain embodiments, the present disclosure provides oligonucleotides comprising linked nucleosides. In such embodiments, nucleosides may be linked together using any internucleoside linkage. The two main classes of internucleoside linking groups are defined by the presence or absence of a phosphorus atom. Representative phosphorus containing internucleoside linkages include, but are not limited to, phosphodiesters (P═O), phosphotriesters, methylphosphonates, phosphoramidate, and phosphorothioates (P═S). Representative non-phosphorus containing internucleoside linking groups include, but are not limited to, methylenemethylimino (—CH₂—N(CH₃)—O—CH₂—), thiodiester (—O—C(O)—S—), thionocarbamate (—O—C(O)(NH)—S—); siloxane (—O—Si(H)₂—O—); and N,N′-dimethylhydrazine (—CH₂—N(CH₃)—N(CH₃)—). Modified linkages, compared to natural phosphodiester linkages, can be used to alter, typically increase, nuclease resistance of the oligonucleotide. In certain embodiments, internucleoside linkages having a chiral atom can be prepared as a racemic mixture, or as separate enantiomers. Representative chiral linkages include, but are not limited to, alkylphosphonates and phosphorothioates. Methods of preparation of phosphorous-containing and non-phosphorous-containing internucleoside linkages are well known to those skilled in the art.

The oligonucleotides described herein contain one or more asymmetric centers and thus give rise to enantiomers, diastereomers, and other stereoisomeric configurations that may be defined, in terms of absolute stereochemistry, as (R) or (S), α or β such as for sugar anomers, or as (D) or (L) such as for amino acids etc. Included in the antisense compounds provided herein are all such possible isomers, as well as their racemic and optically pure forms.

Neutral internucleoside linkages include without limitation, phosphotriesters, methylphosphonates, MMI (3′-CH₂—N(CH₃)—O-5′), amide-3 (3′-CH₂—C(═O)—N(H)-5′), amide-4 (3′-CH₂—N(H)—C(═O)-5′), formacetyl (3′-O—CH₂—O-5′), and thioformacetal (3′-S—CH₂—O-5′). Further neutral internucleoside linkages include nonionic linkages comprising siloxane (dialkylsiloxane), carboxylate ester, carboxamide, sulfide, sulfonate ester and amides (See for example: Carbohydrate Modifications in Antisense Research; Y. S. Sanghvi and P. D. Cook, Eds., ACS Symposium Series 580; Chapters 3 and 4, 40-65). Further neutral internucleoside linkages include nonionic linkages comprising mixed N, O, S and CH₂ component parts.

Additional modifications may also be made at other positions on the oligonucleotide, particularly the 3′ position of the sugar on the 3′ terminal nucleotide and the 5′ position of 5′ terminal nucleotide. For example, one additional modification of the ligand conjugated oligonucleotides of the present disclosure involves chemically linking to the oligonucleotide one or more additional non-ligand moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553), cholic acid (Manoharan et al., Bioorg. Med. Chem. Lett., 1994, 4, 1053), a thioether, e.g., hexyl-5-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 111; Kabanov et al., FEBS Lett., 1990, 259, 327; Svinarchuk et al., Biochimie, 1993, 75, 49), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651; Shea et al., Nucl. Acids Res., 1990, 18, 3777), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923).

Representative United States patents that teach the preparation of such oligonucleotide conjugates include, but are not limited to, U.S. Pat. Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, certain of which are commonly owned, and each of which is herein incorporated by reference.

D. Pharmaceutical Composition and Methods of Delivery

Where clinical applications are contemplated, it will be necessary to prepare pharmaceutical compositions in a form appropriate for the intended application. Generally, this will entail preparing compositions that are essentially free of pyrogens, as well as other impurities that could be harmful to humans or animals. One will generally desire to employ appropriate salts, buffers, and lipids to render delivery of the oligonucleotides to allow for uptake by target cells. Such methods an compositions are well known in the art, for example, as disclosed in U.S. Pat. Nos. 6,747,014 and 6,753,423. Compositions of the present disclosure comprise an effective amount of the oligonucleotide to cells, dissolved or dispersed in a pharmaceutically acceptable carrier or medium.

The phrase “pharmaceutically or pharmacologically acceptable” refers to molecular entities and compositions that do not produce adverse, allergic, or other untoward reactions when administered to an animal or a human. As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, liposomes, cationic lipid formulations, microbubble nanoparticles, and the like. Except insofar as any conventional media or agent is incompatible with the vectors or cells of the present disclosure, its use in therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions.

The active compositions of the present disclosure may include classic pharmaceutical preparations. Administration of these compositions according to the present disclosure will be via any common route so long as the target tissue is available via that route. This includes oral, nasal, buccal, or topical. Alternatively, administration may be by intradermal, subcutaneous, intramuscular, intraperitoneal or intravenous injection, or introduction into the CNS, such as into spinal fluid. Such compositions would normally be administered as pharmaceutically acceptable compositions, described supra.

The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, lipids, nanoparticles, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.

For oral administration the oligonucleotides of the present disclosure may be incorporated with excipients. The compositions of the present disclosure may be formulated in a neutral or salt form. Pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.

Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms such as injectable solutions, drug release capsules and the like. For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, “Remington's Pharmaceutical Sciences” 15th Edition, pages 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Moreover, for human administration, preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biologics standards.

Of particular interest to the present disclosure is the use of lipid delivery vehicles. Lipid vehicles encompass micelles, microemulsions, macroemulsions, liposomes, and similar carriers. The term micelles refers to colloidal aggregates of amphipathic (surfactant) molecules that are formed at a well-defined concentration known as the critical micelle concentration. Micelles are oriented with the nonpolar portions at the interior and the polar portions at the exterior surface, exposed to water. The typical number of aggregated molecules in a micelle (aggregation number) is 50 to 100. Microemulsions are essentially swollen micelles, although not all micellar solutions can be swollen to form microemulsions. Microemulsions are thermodynamically stable, are formed spontaneously, and contain particles that are extremely small. Droplet diameters in microemulsions typically range from 10 100 nm. In contrast, the term macroemulsions refers to droplets with diameters greater than 100 nm. Liposomes are closed lipid vesicles comprising lipid bilayers that encircle aqueous interiors. Liposomes typically have diameters of 25 nm to 1 μm.

In one embodiment of a liposome formulation, the principal lipid of the vehicle may be phosphatidylcholine. Other useful lipids include various natural (e.g., tissue derived L-α-phosphatidyl: egg yolk, heart, brain, liver, soybean) and/or synthetic (e.g., saturated and unsaturated 1,2-diacyl-SN-glycero-3-phosphocholines, 1-acyl-2-acyl-SN-glycero-3-phosphocholines, 1,2-diheptanoyl-SN-glycero-3-phosphocholine) derivatives of the same. Such lipids can be used alone, or in combination with a secondary lipid. Such secondary helper lipids may be non-ionic or uncharged at physiological pH, including non-ionic lipids such as cholesterol and DOPE (1,2-dioleolylglyceryl phosphatidylethanolamine). The molar ratio of a phospholipid to helper lipid can range from about 3:1 to about 1:1, from about 1.5:1 to about 1:1, and about 1:1.

Another specific lipid formulation comprises the SNALP formulation, containing the lipids 3-N—[(ω methoxypoly(ethylene glycol)₂₀₀₀) carbamoyl]-1,2-dimyristyloxy-propylamine (PEG-C-DMA), 1,2-dilinoleyloxy-N,N-dimethyl-3-aminopropane (DLinDMA), 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and cholesterol, in a 2:40:10:48 molar % ratio.

Exemplary amounts of lipid constituents used for the production of the liposome include, for instance, 0.3 to 1 mol, 0.4 to 0.6 mol of cholesterol; 0.01 to 0.2 mol, 0.02 to 0.1 mol of phosphatidylethanolamine; 0.0 to 0.4 mol, or 0-0.15 mol of phosphatidic acid per 1 mol of phosphatidylcholine.

Liposomes can be constructed by well-known techniques. Lipids are typically dissolved in chloroform and spread in a thin film over the surface of a tube or flask by rotary evaporation. If liposomes comprised of a mixture of lipids are desired, the individual components are mixed in the original chloroform solution. After the organic solvent has been eliminated, a phase consisting of water optionally containing buffer and/or electrolyte is added and the vessel agitated to suspend the lipid. Optionally, the suspension is then subjected to ultrasound, either in an ultrasonic bath or with a probe sonicator, until the particles are reduced in size and the suspension is of the desired clarity. For transfection, the aqueous phase is typically distilled water and the suspension is sonicated until nearly clear, which requires several minutes depending upon conditions, kind, and quality of the sonicator. Commonly, lipid concentrations are 1 mg/ml of aqueous phase, but could be higher or lower by about a factor of ten.

Lipids, from which the solvents have been removed, can be emulsified by the use of a homogenizer, lyophilized, and melted to obtain multilamellar liposomes. Alternatively, unilamellar liposomes can be produced by the reverse phase evaporation method (Szoka and Papahadjopoulos, 1978). Unilamellar vesicles can also be prepared by sonication or extrusion. Sonication is generally performed with a bath-type sonifier, such as a Branson tip sonifier (G. Heinemann Ultrashall and Labortechnik, Schwabisch Gmund, Germany) at a controlled temperature as determined by the melting point of the lipid. Extrusion may be carried out by biomembrane extruders, such as the Lipex Biomembrane Extruder (Northern Lipids Inc, Vancouver, British Columbia, Canada). Defined pore size in the extrusion filters may generate unilamellar liposomal vesicles of specific sizes. The liposomes can also be formed by extrusion through an asymmetric ceramic filter, such as a Ceraflow Microfilter (commercially available from the Norton Company, Worcester, Mass.).

Liposomes can be extruded through a small-pore polycarbonate membrane or an asymmetric ceramic membrane to yield a well-defined size distribution. Typically, a suspension is cycled through the membrane one or more times until the desired liposome size distribution is achieved. The liposomes may be extruded through successively smaller-pore membranes, to achieve a gradual reduction in liposome size. For use in the present disclosure, liposomes have a size of about 0.05 microns to about 0.5 microns, or having a size of about 0.05 to about 0.2 microns.

In certain embodiments, the oligonucleotide compounds and compositions as described herein are administered parenterally. In certain embodiments, parenteral administration is by infusion. Infusion can be chronic or continuous or short or intermittent. In certain embodiments, infused pharmaceutical agents are delivered with a pump. In certain embodiments, parenteral administration is by injection.

In certain embodiments, oligonucleotide compounds and compositions are delivered to the CNS. In certain embodiments, oligonucleotide compounds and compositions are delivered to the cerebrospinal fluid. In certain embodiments, oligonucleotide compounds and compositions are administered to the brain parenchyma. In certain embodiments, oligonucleotide compounds and compositions are delivered to an animal by intrathecal administration, or intracerebroventricular administration. Broad distribution of oligonucleotide compounds and compositions, described herein, within the central nervous system may be achieved with intraparenchymal administration, intrathecal administration, or intracerebroventricular administration.

In certain embodiments, parenteral administration is by injection. The injection may be delivered with a syringe or a pump. In certain embodiments, the injection is a bolus injection. In certain embodiments, the injection is administered directly to a tissue, such as striatum, caudate, cortex, hippocampus and cerebellum.

In certain embodiments, delivery of an oligonucleotide compound or composition described herein can affect the pharmacokinetic profile of the oligonucleotide compound or composition. In certain embodiments, injection of a oligonucleotide compound or composition described herein, to a targeted tissue improves the pharmacokinetic profile of the oligonucleotide compound or composition as compared to infusion of the oligonucleotide compound or composition. In a certain embodiment, the injection of an oligonucleotide compound or composition improves potency compared to broad diffusion, requiring less of the compound or composition to achieve similar pharmacology. In certain embodiments, similar pharmacology refers to the amount of time that a target mRNA and/or target protein is down-regulated (e.g., duration of action). In certain embodiments, methods of specifically localizing a pharmaceutical agent, such as by bolus injection, decreases median effective concentration (EC₅₀) by a factor of about 50 (e.g., 50-fold less concentration in tissue is required to achieve the same or similar pharmacodynamic effect). In certain embodiments, methods of specifically localizing a pharmaceutical agent, such as by bolus injection, decreases median effective concentration (EC₅₀) by a factor of 20, 25, 30, 35, 40, 45 or 50.

In certain embodiments, delivery of an oligonucleotide compound or composition, as described herein, to the CNS results in 47% down-regulation of a target mRNA and/or target protein for at least 91 days. In certain embodiments, delivery of a compound or composition results in at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, or at least 75% down-regulation of a target mRNA and/or target protein for at least 20 days, at least 30 days, at least 40 days, at least 50 days, at least 60 days, at least 70 days, at least 80 days, at least 85 days, at least 90 days, at least 95 days, at least 100 days, at least 110 days, at least 120 days. In certain embodiments, delivery to the CNS is by intraparenchymal administration, intrathecal administration, or intracerebroventricular administration.

In certain embodiments, an oligonucleotide is delivered by injection or infusion once every week, every two weeks, every month, every two months, every 90 days, every 3 months, every 6 months, twice a year or once a year.

E. EXAMPLES

The following examples are included to demonstrate preferred embodiments. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent techniques discovered by the inventor to function well in the practice of embodiments, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the disclosure.

Example 1—Results

A time-resolved enhancer activity map. In order to obtain the informative features of eRNA/mRNA dynamics, the inventor performed a large time series GRO-seq analysis of B-lymphoblasts (GM12878) during innate anti-viral immune response. The inventor used Sendai Virus (SeV) to activate the immune response signal-cascade gene induction system as a model to study the anti-viral program. The inventor first combined all GRO-seq data obtained from 12 time points from 0 to 72 hours post-infection to determine a compendium of eRNA-producing enhancers responding to virus, then used HOMER (Heinz et al., 2010) to identify the eRNA transcripts (see Methods). Of 32,832 total intergenic transcripts, 11,025 transcripts overlapped with H3K4me1 or H3K27Ac histone modification peaks, representative enhancer marks (FIG. 1A). The inventor annotated transcription start/termination sites (TSS/TTS) for the 11,025 eRNAs (FIG. 1B). The average predicted length of eRNAs from the inventor's annotation efforts was 1,746 bp (FIG. 7A). Other enhancer marks including p300 and DNase hypersensitivity signals were highly enriched at the TSS of eRNAs (FIG. 1C) (Lai and Pugh, 2017). Additionally, the patterns of H3K4me1 and H3K27Ac ChIP-seq, DNase hypersensitivity and MNase-seq indicated an open chromatin region at the eRNA TSS. Notably, a majority (64%) of the eRNAs were below detection levels prior to virus infection, thereby indicating a dramatic induction of eRNA synthesis upon virus infection (FIG. 1A). This is further supported by the fact that only ˜28% of the inventor's eRNA annotations overlapped with that of the FANTOM5 human enhancer atlas (Andersson et al., 2014), underscoring condition specific differences and. In addition, the inventor found 18,999 intergenic transcripts, lacking initial eRNA production and enhancer marks, being transcribed after infection. These transcripts showed similar lengths as eRNAs defined above (P-value 0.14, t-test). A previous study showed that enhancers initially lacking known enhancer marks, like the 18,999 enhancers that the inventor found here, could acquire enhancer-associated epigenetic modifications upon stimuli (Kaikkonen et al., 2013).

Rapid and dynamic transcriptional response of genes and enhancers. The inventor quantified expression levels of the RefSeq genes and performed differential expression (DE) analysis. Based on the expression dynamics of DE genes (FIG. 2A), the time course can be divided into three stages: 0 h-2 h, limited changes; 4 h-24 h, significant changes with more induced genes (early-up) than repressed; 48 h-72 h, large changes comprised of both up—(late-up) and down—(late-down) regulated genes. To understand these expression dynamics more meaningfully, the inventor performed gene ontology (GO) analysis at each time point (FIG. 7B). DE gene-enriched functions were highly consistent between time points within each of the three stages. For example, the most frequently enriched GO terms of early-up, late-up and late-down groups were “responses to virus,” “apoptosis” and “cell cycle,” respectively. The inventor also performed DE analysis with the annotated eRNAs. Their expression dynamics could also be divided into three stages, exactly matching those of DE genes (FIG. 2B). Representative examples of inducible genes and eRNAs are shown in FIGS. 7C and 7D. Furthermore, nearest genes of the inducible eRNAs (described in the section describing enhancer-promoter pairs) were functionally enriched in immune system processes (FIG. 2C).

To visualize and verify the dynamics of eRNA and gene expression patterns, the inventor performed principal component analysis (PCA), which showed a trajectory of cellular states (FIGS. 2D-E). The first two principal components (PC) clearly separated samples from each time points. Principal component 2 (PC2) values showed an interesting trajectory, which moved away from the baseline in early time and returned after 18 h, matching the expression dynamics of immune related genes (GO term “defense response to virus,” P-value 2.5E-12). Similar analysis was performed for genes correlated with PC1, showing enrichment of GO terms “translation,” “apoptosis,” and “RNA decay.” Likewise, the first two PCs of eRNAs showed similar dynamics as those of gene expression, indicating connected regulatory processes between eRNA and gene expression. In addition, t-distributed stochastic neighbor embedding (t-SNE) (Jamieson et al., 2010) result showed almost identical patterns. (FIGS. 7E-F).

Cytokine IFNB1 as a representative transient transcript. As a representative virus-inducible case, the inventor investigated the IFNB1 gene and its enhancer L2, which the inventor previously identified as a novel virus inducible long-range enhancer regulating IFNB1 transcription in IMR90 lung fibroblasts (Banerjee et al., 2014). An independent study (Decque et al., 2016) has also demonstrated that the L2 is a major enhancer regulating IFNB1 expression in bone marrow derived dendritic cells and macrophages. The inventor's GRO-seq data in GM12878 cells indicate strong transcription at IFNB1 and the L2 element in early time points just after SeV infection (FIGS. 8A-B). L2 eRNA was transcribed first at 1 hour and then IFNB1 transcript emerged around 1 hour after L2, implying that eRNA generation precedes target gene transcription. Interestingly, L2 transcription continues to be detected even at 72 hours post infection when IFNB1 has become repressed by post-induction repression mechanisms (Ren et al., 1999), implicating a potentially novel enhancer inactivation and decommissioning mechanism. The inventor also investigated other well-known transcription factors of IRF and NFκB families which are also up-regulated at these earliest time points (FIG. 8B).

Construction of an enhancer-target gene map for viral response. Accurate cell-specific and genome-wide enhancer target identification is a challenging task. Despite several improvements in the past few years (Cao et al., 2017; Jin et al., 2013; Whalen et al., 2016), the accuracy is still far from satisfactory for in-depth case studies of individual genes or enhancers. Using metagene analysis, these results, as well as several other studies (Hah et al., 2013 and Kaikkonen et al., 2013), have shown the coordinated transcriptional dynamics of enhancers and neighbor genes should be highly enriched with functional targets. Can one take advantage of the paired expression profiles to further refine target prediction for individual enhancers? To this end, the inventor carefully examined the expression profiles of eRNA/gene pairs that were significantly activated by SeV infection. In addition to the expected, correlated pattern of concordant on/off behaviors between enhancers and genes, the inventor also observed a discordant expression pattern showing persistent eRNA transcription after target gene repression (FIG. 3A). Interestingly, this discordant pattern was exhibited by the previously validated L2-IFNB1 EP (enhancer-promoter) pair. Thus, the co-inducibility of eRNAs and target genes is a potentially important feature for inferring functional enhancer targets, regardless of regulatory divergence of the concordant and discordant sets of eRNA/gene pairs. To identify inducible enhancers and genes, the inventor constructed two indices: the continuity index (CI) and the amplitude index (AI) (FIG. 3B; see Example 3). The CI index is used to filter out random fluctuations in the expression levels, especially for eRNAs which are lowly expressed and more subject to technical variability. The AI index is designed to represent the maximum induced levels, which is stable with respect to the specific expression patterns but can be highly variable for each EP pair. 299 genes and 787 enhancers were identified as inducible. Consistent with the induced transcriptional activity, the H3K27Ac levels of these 787 enhancers were also induced by SeV infection (FIG. 7G). Genomic proximity is also an important factor for identifying enhancer targets (Sanyal et al., 2012). The inventor found that inducible genes were highly enriched within 200 Kb from the inducible enhancers (FIG. 3C) and vice versa (FIG. 9A). The inventor assigned the inducible enhancers with the nearest inducible genes within 200 Kb and obtained 123 highly confident enhancer-promoter (EP) pairs (Supplemental Table S1). Extending the proximity window farther enabled us to define more enhancer-promoter pairs, but this increased sensitivity of identifying more EP pairs also resulted in significant increases in the false positive rate for the inventor's inducible EP prediction. For example, the percentage of inducible genes decreased from ˜50% to ˜30% if the distance threshold was increased by another 100 Kb. In addition, the current analysis focused only on the mRNA encoding target genes and excluded possible target genes encoding noncoding RNAs due to the limited functional information regarding these genes. This highly prioritized inducible eRNA and target gene set included not only the previously validated L2-IFNB1 pair, but also other critical genes involved in immune function such as the CD38, IRF8, TNFSF10 and TLR7 genes, whose distal regulatory elements were largely unknown.

TABLE S1 All predicted induced eRNAs and their target genes. Target_gene Target_gene(Refseq) Enhancer_id (symbol) enh_hg19 NM_002036 MetaEnhancer_1136_+ ACKR1 chr1 158975648 158977353 NM_001122951 MetaEnhancer_1136_+ ACKR1 chr1 158975648 158977353 NM_004833 MetaEnhancer_1136_+ AIM2 chr1 158975648 158977353 NM_001136540 MetaEnhancer_1799_− APOL1 chr22 36805195 36806192 NM_001136540 MetaEnhancer_862_− APOL1 chr22 36846877 36848115 NM_030882 MetaEnhancer_1799_− APOL2 chr22 36805195 36806192 NM_145637 MetaEnhancer_1799_− APOL2 chr22 36805195 36806192 NM_030641 MetaEnhancer_3137_− APOL6 chr22 36030413 36031205 NM_174919 MetaEnhancer_2379_− ARHGAP27 chr17 43433743 43435137 NM_001128616 MetaEnhancer_2422_+ ARHGEF3 chr3 56726327 56729181 NM_019555 MetaEnhancer_2422_+ ARHGEF3 chr3 56726327 56729181 NM_001731 MetaEnhancer_3101_+ BTG1 chr12 92586863 92587704 NM_001295 MetaEnhancer_258_− CCR1 chr3 46149958 46152633 NM_001295 MetaEnhancer_1961_+ CCR1 chr3 46150916 46156022 NM_001775 MetaEnhancer_3795_− CD38 chr4 15757373 15758209 NM_001775 MetaEnhancer_847_− CD38 chr4 15767579 15773083 NM_001775 MetaEnhancer_1694_+ CD38 chr4 15773236 15774381 NM_001243794 MetaEnhancer_2191_+ CHST12 chr7 2439830 2441170 NM_172210 MetaEnhancer_3084_+ CSF1 chr1 110435830 110436993 NM_172212 MetaEnhancer_3084_+ CSF1 chr1 110435830 110436993 NM_000757 MetaEnhancer_3084_+ CSF1 chr1 110435830 110436993 NM_138287 MetaEnhancer_2972_− DTX3L chr3 122380136 122380883 NM_001034194 MetaEnhancer_2326_− EXOSC9 chr4 122708957 122710268 NM_001034194 MetaEnhancer_1507_− EXOSC9 chr4 122714858 122717023 NM_001034194 MetaEnhancer_1473_+ EXOSC9 chr4 122716718 122718546 NM_153230 MetaEnhancer_2571_− FBXO39 chr17 6842901 6843791 NM_014824 MetaEnhancer_94_+ FCHSD2 chr11 72864171 72888511 NM_002053 MetaEnhancer_1625_+ GBP1 chr1 89546827 89547678 NM_052941 MetaEnhancer_1625_+ GBP4 chr1 89546827 89547678 NM_052941 MetaEnhancer_2172_+ GBP4 chr1 89739974 89742358 NM_001206567 MetaEnhancer_1136_+ IFI16 chr1 158975648 158977353 NM_002038 MetaEnhancer_1613_− IFI6 chr1 28014868 28016573 NM_001270927 MetaEnhancer_2029_− IFIT1 chr10 91052142 91055958 NM_001270927 MetaEnhancer_3024_+ IFIT1 chr10 91055858 91057638 NM_001547 MetaEnhancer_4002_− IFIT2 chr10 90922933 90923624 NM_001547 MetaEnhancer_1253_+ IFIT2 chr10 90923524 90925010 NM_001547 MetaEnhancer_2029_− IFIT2 chr10 91052142 91055958 NM_001547 MetaEnhancer_3024_+ IFIT2 chr10 91055858 91057638 NM_001289758 MetaEnhancer_4002_− IFIT3 chr10 90922933 90923624 NM_001031683 MetaEnhancer_4002_− IFIT3 chr10 90922933 90923624 NM_001289758 MetaEnhancer_1253_+ IFIT3 chr10 90923524 90925010 NM_001031683 MetaEnhancer_1253_+ IFIT3 chr10 90923524 90925010 NM_001289758 MetaEnhancer_2029_− IFIT3 chr10 91052142 91055958 NM_001031683 MetaEnhancer_2029_− IFIT3 chr10 91052142 91055958 NM_001289758 MetaEnhancer_3024_+ IFIT3 chr10 91055858 91057638 NM_001031683 MetaEnhancer_3024_+ IFIT3 chr10 91055858 91057638 NM_012420 MetaEnhancer_2029_− IFIT5 chr10 91052142 91055958 NM_012420 MetaEnhancer_3024_+ IFIT5 chr10 91055858 91057638 NM_003641 MetaEnhancer_1268_+ IFITM1 chr11 188083 189410 NM_003641 MetaEnhancer_1341_− IFITM1 chr11 347562 351028 NM_003641 MetaEnhancer_230_− IFITM1 chr11 353806 356185 NM_006435 MetaEnhancer_1268_+ IFITM2 chr11 188083 189410 NM_006435 MetaEnhancer_1341_− IFITM2 chr11 347562 351028 NM_006435 MetaEnhancer_230_− IFITM2 chr11 353806 356185 NM_002176 MetaEnhancer_1571_+ IFNB1 chr9 21096515 21098279 NM_002198 MetaEnhancer_250_− IRF1 chr5 131828856 131832505 NM_002198 MetaEnhancer_372_+ IRF1 chr5 131831379 131847154 NM_002163 MetaEnhancer_2143_+ IRF8 chr16 85922550 85923645 NM_002163 MetaEnhancer_259_+ IRF8 chr16 86028925 86034443 NM_005547 MetaEnhancer_3423_+ IVL chr1 152844459 152845369 NM_005547 MetaEnhancer_2511_+ IVL chr1 152940836 152941593 NM_001162895 MetaEnhancer_633_− KIAA0040 chr1 175173105 175173615 NM_001162893 MetaEnhancer_633_− KIAA0040 chr1 175173105 175173615 NM_001162895 MetaEnhancer_1625_− KIAA0040 chr1 175201951 175206691 NM_001162893 MetaEnhancer_1625_− KIAA0040 chr1 175201951 175206691 NM_001162895 MetaEnhancer_3581_− KIAA0040 chr1 175255261 175256747 NM_001162893 MetaEnhancer_3581_− KIAA0040 chr1 175255261 175256747 NM_001162895 MetaEnhancer_1115_+ KIAA0040 chr1 175256708 175258040 NM_001162893 MetaEnhancer_1115_+ KIAA0040 chr1 175256708 175258040 NM_002308 MetaEnhancer_606_− LGALS9 chr17 26131567 26137792 NM_002308 MetaEnhancer_211_+ LGALS9 chr17 26135260 26137784 NM_002308 MetaEnhancer_421_+ LGALS9 chr17 26137777 26140602 NM_002432 MetaEnhancer_1136_+ MNDA chr1 158975648 158977353 NM_013262 MetaEnhancer_3166_+ MYLIP chr6 15989743 15990881 NM_022750 MetaEnhancer_1844_+ PARP12 chr7 139910100 139913318 NM_017554 MetaEnhancer_2972_− PARP14 chr3 122380136 122380883 NM_001146102 MetaEnhancer_2972_− PARP9 chr3 122380136 122380883 NM_001146104 MetaEnhancer_2972_− PARP9 chr3 122380136 122380883 NM_001146103 MetaEnhancer_2972_− PARP9 chr3 122380136 122380883 NM_001146106 MetaEnhancer_2972_− PARP9 chr3 122380136 122380883 NM_021105 MetaEnhancer_4023_− PLSCR1 chr3 146268426 146269080 NM_002787 MetaEnhancer_1544_− PSMA2 chr7 43110543 43112396 NM_006871 MetaEnhancer_844_− RIPK3 chr14 24741839 24743689 NM_001193307 MetaEnhancer_3039_+ SAMD9 chr7 92666321 92666833 NM_001303496 MetaEnhancer_3039_+ SAMD9L chr7 92666321 92666833 NM_015474 MetaEnhancer_1375_− SAMHD1 chr20 35493353 35495639 NM_015295 MetaEnhancer_510_− SMCHD1 chr18 2634970 2637532 NM_015295 MetaEnhancer_730_− SMCHD1 chr18 2637665 2641759 NM_013306 MetaEnhancer_2509_+ SNX15 chr11 64918212 64918934 NM_001308205 MetaEnhancer_2826_+ SSR3 chr3 156323933 156325284 NM_001308204 MetaEnhancer_2826_+ SSR3 chr3 156323933 156325284 NM_001308197 MetaEnhancer_2826_+ SSR3 chr3 156323933 156325284 NM_001308205 MetaEnhancer_2114_+ SSR3 chr3 156361733 156363160 NM_001308204 MetaEnhancer_2114_+ SSR3 chr3 156361733 156363160 NM_001308197 MetaEnhancer_2114_+ SSR3 chr3 156361733 156363160 NM_001308205 MetaEnhancer_3846_+ SSR3 chr3 156374076 156375609 NM_001308204 MetaEnhancer_3846_+ SSR3 chr3 156374076 156375609 NM_001308197 MetaEnhancer_3846_+ SSR3 chr3 156374076 156375609 NM_016562 MetaEnhancer_341_− TLR7 chrX 12859229 12863555 NM_016562 MetaEnhancer_502_+ TLR7 chrX 12862239 12865018 NM_001190942 MetaEnhancer_2005_+ TNFSF10 chr3 172194931 172195631 NM_001190943 MetaEnhancer_2005_+ TNFSF10 chr3 172194931 172195631 NM_001190942 MetaEnhancer_3924_− TNFSF10 chr3 172263822 172264784 NM_001190943 MetaEnhancer_3924_− TNFSF10 chr3 172263822 172264784 NM_001190942 MetaEnhancer_3404_− TNFSF10 chr3 172295508 172299753 NM_001190943 MetaEnhancer_3404_− TNFSF10 chr3 172295508 172299753 NM_001190942 MetaEnhancer_734_− TNFSF10 chr3 172308346 172310066 NM_001190943 MetaEnhancer_734_− TNFSF10 chr3 172308346 172310066 NM_001190942 MetaEnhancer_116_+ TNFSF10 chr3 172310235 172315325 NM_001190943 MetaEnhancer_116_+ TNFSF10 chr3 172310235 172315325 NM_001190942 MetaEnhancer_811_− TNFSF10 chr3 172310301 172313961 NM_001190943 MetaEnhancer_811_− TNFSF10 chr3 172310301 172313961 NM_025195 MetaEnhancer_733_− TRIB1 chr8 126614669 126617093 NM_001282985 MetaEnhancer_733_− TRIB1 chr8 126614669 126617093 NM_025195 MetaEnhancer_1012_+ TRIB1 chr8 126617345 126619945 NM_001282985 MetaEnhancer_1012_+ TRIB1 chr8 126617345 126619945 NM_030961 MetaEnhancer_931_+ TRIM56 chr7 100893754 100895706 NM_001301144 MetaEnhancer_501_− TRIM69 chr15 45073139 45076695 NM_001301144 MetaEnhancer_1609_+ TRIM69 chr15 45076646 45078317 NM_020830 MetaEnhancer_512_− WDFY1 chr2 224812655 224817461 NM_017523 MetaEnhancer_2571_− XAF1 chr17 6842901 6843791 NM_001160417 MetaEnhancer_1451_+ ZBP1 chr20 56008141 56009316 NM_001160419 MetaEnhancer_1451_+ ZBP1 chr20 56008141 56009316

TABLE S2 Genomic information for eRNAs and target genes of induced EP pairs tested eRNA Whole region High enrichment region Target Genes enhancer ID strand chr start end chr start end eRNA length Gene name strand MetaEnhancer_1136_+ + chr 1 157242272 157243977 chr 1 157242460 157242561 1705 ACKR1 + MetaEnhancer_258_− − chr 3 46124962 46127637 chr 3 46127469 46127636 2675 CCR1 − MetaEnhancer_1694_+ + chr 4 15382334 15383479 chr 4 15382463 15382581 1145 CD38-1 + MetaEnhancer_3795_− − chr 4 15366471 15367307 chr 4 15366966 15367155 836 CD38-2 + MetaEnhancer_1136_+ + chr 1 157242272 157243977 chr 1 157242460 157242561 1705 IFI16 + MetaEnhancer_1571_+ + chr 9 21086515 21088279 chr 9 21086643 21086794 1764 IFNB1 − MetaEnhancer_259_+ + chr 16 84586426 84591944 chr 16 84586456 84586609 5518 IRF8 + MetaEnhancer_1115_+ + chr 1 173523331 173524663 chr 1 173523395 173523541 1332 KIAA0040 − MetaEnhancer_1136_+ + chr 1 157242272 157243977 chr 1 157242460 157242561 1705 MNDA + MetaEnhancer_2972_− − chr 3 123862826 123863573 chr 3 123863236 123863394 747 PARP14 + MetaEnhancer_2972_− − chr 3 123862826 123863573 chr 3 123863233 123863404 747 PARP9 − MetaEnhancer_3039_+ + chr 7 92504257 92504769 chr 7 92504452 92504536 512 SAMD9 − MetaEnhancer_502_+ + chr X 12772160 12774939 chr X 12772218 12772389 2779 TLR7-1 + MetaEnhancer_341_− − chr X 12769150 12773476 chr X 12771691 12771969 4326 TLR7-2 + MetaEnhancer_116_+ + chr 3 173792929 173798019 chr 3 173796865 173797019 5090 TNFSF 10-1 − MetaEnhancer_734_− − chr 3 173791040 173792760 chr 3 173792248 173792364 1720 TNFSF 10-2 − MetaEnhancer_2005_+ + chr 3 173677625 173678325 chr 3 173677765 173677876 700 TNFSF 10-3 − MetaEnhancer_512_− − chr 2 224520899 224525705 chr 2 224525490 224525639 4806 WDFY1 − eRNA Whole region First exon region gene enhancer ID chr start end chr start end length MetaEnhancer_1136_+ chr 1 157440426 157442914 chr 1 1.6E+08 1.6E+08 2488 MetaEnhancer_258_− chr 3 46218203 46224836 chr 3 4.6E+07 4.6E+07 6633 MetaEnhancer_1694_+ chr 4 15389028 15459804 chr 4 1.5E+07 1.5E+07 70776 MetaEnhancer_3795_− chr 4 15389028 15459804 chr 4 1.5E+07 1.5E+07 70776 MetaEnhancer_1136_+ chr 1 157246305 157291569 chr 1 1.6E+08 1.6E+08 45264 MetaEnhancer_1571_+ chr 9 21067103 21067943 chr 9 2.1E+07 2.1E+07 840 MetaEnhancer_259_+ chr 16 84490274 84513712 chr 16 8.4E+07 8.4E+07 23438 MetaEnhancer_1115_+ chr 1 173392745 173428852 chr 1 1.7E+08 1.7E+08 36107 MetaEnhancer_1136_+ chr 1 157067791 157085894 chr 1 1.6E+08 1.6E+08 18103 MetaEnhancer_2972_− chr 3 123882361 123932377 chr 3 1.2E+08 1.2E+08 50016 MetaEnhancer_2972_− chr 3 123729449 123766213 chr 3 1.2E+08 1.2E+08 36764 MetaEnhancer_3039_+ chr 7 92566761 92585272 chr 7 9.3E+07 9.3E+07 18511 MetaEnhancer_502_+ chr X 12795122 12818401 chr X 1.3E+07 1.3E+07 23279 MetaEnhancer_341_− chr X 12795122 12818401 chr X 1.3E+07 1.3E+07 23279 MetaEnhancer_116_+ chr 3 173705991 173723991 chr 3 1.7E+08 1.7E+08 18000 MetaEnhancer_734_− chr 3 173705991 173723991 chr 3 1.7E+08 1.7E+08 18000 MetaEnhancer_2005_+ chr 3 173705991 173723991 chr 3 1.7E+08 1.7E+08 18000 MetaEnhancer_512_− chr 2 224448308 224518296 chr 2 2.2E+08 2.2E+08 69988

TABLE S3 Genomic information for eRNAs and target genes of control EP pairs tested. eRNA Whole region High enrichment region Target Genes enhancer ID strand chr start end chr start end eRNA length Gene name strand MetaEnhancer_600_+ + chr 22 37680218 37682221 chr 22 37680446 37680578 2003 APOBE C3B + MetaEnhancer_600_+ + chr 22 37680218 37682221 chr 22 37680446 37680578 2003 APOBE C3D-1 + MetaEnhancer_94_− − chr 22 37677998 37680141 chr 22 37679910 37680116 2143 APOBE C3D-2 + MetaEnhancer_1529_+ + chr 6 47490687 47491589 chr 6 47490697 47490886 902 CD2AP + MetaEnhancer_699_+ + chr 5 118395014 118397954 chr 5 118395699 118396002 2940 DMXL1-1 + MetaEnhancer_454_− − chr 5 118393146 118393146 chr 5 118396304 118396575 3465 DMXL1-2 + MetaEnhancer_475 _+ + chr 6 33103702 33105577 chr 6 33105577 33105889 3627 HLA-DMA − MetaEnhancer_157_− − chr 6 32546422 32549330 chr 6 32548510 32548783 2908 HLA-DRA + MetaEnhancer_157_− − chr 6 32546422 32549330 chr 6 32548510 32548783 2908 HLA-DRBS − MetaEnhancer_820_− − chr 17 38333528 38334970 chr 17 38334705 38334946 1442 IFI35 + MetaEnhancer_311_+ + chr 17 34064382 34065788 chr 17 34064375 34064679 1406 MLLT6 + MetaEnhancer_544_− − chr 13 76886469 76887807 chr 13 76887554 76887756 1338 MYCBP2 − MetaEnhancer_327_+ + chr 2 64303953 64307226 chr 2 64303970 64304149 3273 PELI1 − MetaEnhancer_1477_− − chr 16 11297248 11299746 chr 16 11297809 11297902 2498 SOCS1-1 − MetaEnhancer_810 − − chr 16 11308132 11312802 chr 16 11312513 11312648 4670 SOCS1-2 − MetaEnhancer_1228_+ + chr 20 55489469 55491648 chr 20 55489512 55489777 2179 ZBP1 − MetaEnhancer_804_+ + chr 18 58324203 58326493 chr 18 58324896 58325080 2290 ZCCHC2 + MetaEnhancer_246 _+ + chr 15 78096744 78104705 chr 15 78100853 78101069 7961 ZFAND6 + eRNA Whole region First exon region gene enhancer ID chr start end chr start end length MetaEnhancer_600_+ chr 22 37708349 37718730 chr 22 3.8E+07 3.8E+07 10381 MetaEnhancer_600_+ chr 22 37747063 37759202 chr 22 3.8E+07 3.8E+07 12139 MetaEnhancer_94_− chr 22 37747063 37759202 chr 22 3.8E+07 3.8E+07 12139 MetaEnhancer_1529_+ chr 6 47553483 47702955 chr 6 4.8E+07 4.8E+07 149472 MetaEnhancer_699_+ chr 5 118434982 118612721 chr 5 1.2E+08 1.2E+08 177739 MetaEnhancer_454_− chr 5 118434982 118612721 chr 5 1.2E+08 1.2E+08 177739 MetaEnhancer_475 _+ chr 6 33024368 33028877 chr 6 3.3E+07 3.3E+07 4509 MetaEnhancer_157_− chr 6 32515596 32520802 chr 6 3.3E+07 3.3E+07 5206 MetaEnhancer_157_− chr 6 32593131 32605984 chr 6 3.3E+07 3.3E+07 12853 MetaEnhancer_820_− chr 17 38412267 38420002 chr 17 3.8E+07 3.8E+07 7735 MetaEnhancer_311_+ chr 17 34115398 34139582 chr 17 3.4E+07 3.4E+07 24184 MetaEnhancer_544_− chr 13 76516792 76799178 chr 13 7.7E+07 7.7E+07 282386 MetaEnhancer_327_+ chr 2 64173289 64225109 chr 2 6.4E+07 6.4E+07 51820 MetaEnhancer_1477_− chr 16 11255774 11257540 chr 16 1.1E+07 1.1E+07 1766 MetaEnhancer_810 − chr 16 11255774 11257540 chr 16 1.1E+07 1.1E+07 1766 MetaEnhancer_1228_+ chr 20 55612307 55629038 chr 20 5.6E+07 5.6E+07 16731 MetaEnhancer_804_+ chr 18 58341637 58396798 chr 18 5.8E+07 5.8E+07 55161 MetaEnhancer_246 _+ chr 15 78138964 78217790 chr 15 7.8E+07 7.8E+07 78826

Inducible enhancers have conserved sequences. Since enhancers activate their target genes by recruiting transcriptional factors (TF), the inventor hypothesized that these inducible enhancers might have distinct TF binding motifs supporting virus inducible gene regulation. The inventor analyzed human TF motif occurrences within the inducible enhancers and found a strong enrichment of binding sites for IRF- and STAT-family proteins, which are known interferon responsive factors (FIGS. 3D-E). In addition, IRF7 and STAT2 were up-regulated by more than 2-fold post SeV treatment (FIG. 3E). Most TF with high motif enrichment reached 50% of their maximum expression levels no later than 6 hours after virus infection (FIG. 3E), thus supporting the inventor's hypothesis of enhancer induction through TF activation.

These inducible enhancers, interestingly, showed a significantly higher evolutionary sequence conservation level than carefully selected background regions (FIG. 3F; FIGS. 9B-C), especially near the TSS of eRNAs. Synteny of enhancer and promoters across 11 species spanning the vertebrate phylogenetic tree was also examined (see Example 3). The inventor found that the induced EP pairs had ˜10% higher chance than the random background to be immobilized on the same chromosome across the 11 vertebrate genomes (FIG. 3G). Moreover, the induced pairs showed a higher probability to remain in close proximity to each other (<500 Kb; FIG. 9D).

Dynamic physical EP association correlated with target gene expression patterns. Physical interaction between an enhancer and its target promoter has been accepted as a general mechanism of gene activation. It is thought that many inducible genes are regulated through pre-existing interactions with enhancers (Jin et al., 2013); however, the fate of these interactions after induction when the gene is turned off has not been adequately addressed. The inventor examined the dynamic physical interaction of 18 inducible EP pairs using a time course chromosome conformation capture (3C) assays. The inventor also sampled 18 active enhancers and genes within 200 Kb that did not pass the inducibility criterion as a control set (Supplemental Tables S2 and S3). Most inducible EP pairs showed the highest interaction between enhancer and promoter at 12 hours (FIG. 4A). This transient physical interaction correlated with the corresponding target gene expression profiles (FIG. 4C). In contrast, the control pairs showed highly variable interaction patterns during the time course and a lower inducibility of physical interaction (FIGS. 4A-B). The inducible EP pairs showed a significantly higher inducible interaction frequency (Kolmogorov-Smirnov test, P-value=0.0286; FIG. 4B). A notable observation from this analysis is that, in most cases, a decrease in physical interaction after 12 hours post infection coincided with a concomitant decrease in target gene transcription. Thus, this transient physical EP interaction may determine the maximal promoter activity. In addition, some eRNAs can continue to be transcribed beyond 12 hours post infection (FIGS. 11A-C), as in the case for the IFNB1 and L2 and many other EP pairs. Therefore, physical dissociation of an enhancer from its target promoter might be a critical mechanism of post-induction repression of these target genes, irrespective of the status of eRNA synthesis at the enhancers.

Functional relevance of eRNA expression on target gene activation. Although many eRNAs have been shown to be important for target promoter regulation by a number of studies (Li et al., 2013; Melo et al., 2013; Mousavi et al., 2013), there is an emerging debate concerning the general functionality of eRNAs from several studies that suggest eRNAs are dispensable for enhancer function (Engreitz et al., 2016; Hah et al., 2013; Kaikkonen et al., 2013; Rahman et al., 2017). To examine the functional relevance of the inducible eRNAs that the inventor has identified, he employed systematic siRNA-mediated eRNA knockdown (KD) assays and determined their target gene expression before and after siRNA transfection. In total, the inventor used 85 siRNAs for depleting eRNAs of both induced and control EP pairs (Supplemental Tables S5, S6). 49 siRNAs were able to reduce eRNA expression levels from 28 enhancers (FIG. 10A; eRNA fold-change (eFold)<1). The inventor performed statistical analysis and determined eFold<0.7 as a reasonable threshold for assessing the effectiveness of eRNA KD experiments (FIG. 4D). 11 inducible and 12 control EP pairs that passed this threshold were further examined. Interestingly, all target genes in the inducible EP pairs were repressed by eRNA KD (FIG. 4E, left). In contrast, half of target genes from the control EP pairs were not repressed, and some were even activated upon eRNA reduction (FIG. 4E, right). Representative cases from the inducible EP pairs are shown in FIG. 4F. Similar to the inventor's 3C results, this knockdown analysis of eRNAs demonstrates that the inducible eRNAs are biochemically functional in mediating target gene activation.

Inducible eRNAs promote physical interaction with the target promoter. According to the inventor's current 3C results and the results of previous reported studies (Banerjee et al., 2014; Schaukowitch et al., 2014), the transient physical association pattern was highly correlated with the transient transcription pattern of the target genes (FIG. 4A). Also, the eRNA KD results indicated functional relevance of these inducible eRNAs in the target gene transcription (FIG. 4E). Based on these results, the inventor investigated if eRNAs play a general role in mediating physical interactions. The inventor first analyzed the physical higher order chromatin interactions by 3C assay upon eRNA KD of the IFNB1 gene. This led to decreased physical interaction of the enhancer with the promoter by about 20% (FIG. 11A). The inventor also examined the TNFSF10 locus containing three distinct inducible enhancers, enabling us to examine the effect of single eRNA KD on multiple EP interactions. Single eRNA KD led to dissociation of the corresponding enhancer from the promoter, as well as reduced interaction between the other enhancers and the TNFSF10 promoter (Interaction A-B in FIGS. 11A-B) and among the three enhancers (Interaction C in FIGS. 5A-B). The IFI35 and MYCBP2 EP pairs were analyzed as control pairs (FIGS. 11B-C). Their eRNA KD did not affect the interaction between the enhancer and the promoter. Surprisingly, MYCBP2 eRNA KD resulted in an increase of EP interaction and the elevated target gene expression levels. This observation was not a unique case, as the inventor has identified a number of eRNAs with similar functional profiles (FIG. 4E), suggesting there may be diverse classes of eRNAs (i.e., activator- and repressor-eRNAs). From these targeted studies, inducible eRNAs exhibit a strong physical and functional association with the target genes. In contrast, non-inducible eRNAs exhibit much weaker functional and physical association with the target genes.

Multiple eRNAs collaborate for regulating target gene transcription. Since genes can be regulated by a combination of multiple enhancers (Joo et al., 2016), the inventor asked how might multiple inducible eRNAs coordinate their action on their target gene. He performed combinatorial eRNA KD by applying combined siRNAs to determine how eRNAs may function together. He examined the TNFSF10 gene, which has three inducible enhancers based on the inventor's analysis (#5, #30, and #38; FIG. 5A; Table 1 and Sequence Listing). Single eRNA KD decreased EP interaction and TNFSF10 transcription (FIGS. 5B-C). However, the effects on the levels of other eRNAs showed a complex pattern (FIG. 5C): #5KD reduced #38 but increased #30; #30KD decreased #38 but increased #5; #38KD reduced #5 but increased #30. One clear pattern from this analysis is that there is a reciprocal and compensatory relationship between #5 and #30 eRNAs, which are bidirectional divergent transcripts originating from a single enhancer. This reciprocal effect was also observed in the inventor's previous work on the L2 enhancer (Banerjee et al., 2014). When all three siRNAs were combined, all three eRNAs decreased, as well as the target TNFSF10 mRNA (FIG. 5C). The inventor also analyzed the TLR7 and CD38 genes, each with two inducible eRNAs (FIGS. 12A-B). Overlapping bidirectional eRNAs from TLR7 also showed the reciprocal effect under single eRNA KD. In the case of CD38, one eRNA (#37) seems to be more dominant than the other in its contribution to the target gene activation. For both TLR7 and CD38, double KD of eRNAs reduced the corresponding mRNA expression incrementally. Taken together, these targeted analyses demonstrate how inducible eRNAs collaborate to support their target gene transcription. Overlapping, bidirectional eRNAs represent an interesting class of eRNAs displaying a compensating expression pattern upon knockdown and likely serve redundant roles to maintain the target gene expression. In addition, the transcriptional direction of eRNAs does not seem to be an important factor in determining their functional contribution to target gene expression.

TABLE 1 TNFSF10 SEQUENCE LISTING SEQ ID NO: 1; LENGTH: 5090; TYPE: DNA; ORGANISM: Homo sapiens ataccagtgtagtgactgggacctttgttccttccccagcctgaggtctgttagggcagtaccactgcaactgcagaggcgaagg tttgtgggttcactctggtatttatttcctcttcgaagaaatgcgggggtgcctctgattgaagtggtcaggcggaaacaggatg gtggtgctggagtctcaggtcgggcagccctatgcagtgaggactgggacttgtggggaacagtctgaccgcttttctaaggtgg gcgctctgtgctgggggtctggaccagcccctggtactcacagaggacttttcagagcctggagacagtaagggcaagggctgc aagacagcaaacatcacaccccccaccctctcaccccccaacccccaaacactgggagcgctgtcccagagagttatggagct gctactggctcaatatccctggcagggggtgggtggagacccaggccaggaggactcatccagtgaggagaaacaggtttggag acttgtgtaaaaaagcagtctggccacttttccacaggacagccatgttgtgctggggggtccactccagtcactgatggatca ccttgcactctctaaagcctgaaggcaacaaggactgaggctgtgaaacagcaaagatggccgcctaccccttcctctgagagc tccctctcagggatgtgtaatgctgctaccagcagctggctagagttccaagccagtgggtcttatcctgtgacctctgaagtgc tatggaagtgaggcctgcagatcatcgctgctcagccccctggattcagcccctttcataggagtaggtatgggggtctaacctc ccacttggctggagtagcagttacttttgccaggaagccaggatatctaaggctcctggggctccgtgtgtacctgagcggctgc tctgccaagactccccatagctctgtgtatctgactgaaggccctagtggagtgggttcatgaggggatctcctgacccaagagt agcaacgatccatgggagaagcattggtccgcagggtcgctcattcactcacggcttccctggatggggaggttcccctggctcc atgtttctcccgtgtgggcggttgtcctgccctgcttttctccattctccatgggtcaggttgttttcttgatgaattccaacat gtgtatctgtatgtttcggttgaaagtgcagtatttactcgccccatctatttctctctgtgagagcagtacacactagctgctt ctggttgagcgtaagaaaaataaatgcccttttaatgtgtttgctagaagatagaaaacattgcaaagaacagagtagaattcat attcttaaaaacaaatatgaaaacttattctactttccttctttaccaatgaaaataaacatatttattgtcctcaatgcacttt tttctttgaaataataactcctcagaaagaccgttgcagttaagaatatcagctgtcacacagagctaaatccttttaattgtga attttttccccacaaagcatgatgaactacgtcttgacagggcaggcaaagtattaaagtaaaatatttttccccacattttatt tttcttttctttctttctttcctttttttttttttttttttttttgagatggagtttcactcttgttgtccaggctggagtgcaa tggcgtgatctcagctcactgcaacctccacctcctgggttcaagcaattctcctgcctcagcctctggtgtagctgggattaca ggcacacgccaccacgcctggctaatttttgtatttttagcagagatgggatttcaccacattggccaagctggtctcaaactcc tgacctcagtgatccatctgcctcagcctcccaaagtgctgggattacaggtgtgagccactgcgcccagcccccattttctgag gtgaaatgaaggaagagttaatcattcatgctccttttcttgggttcagctgccatccttacttacctctgatggaggactaggg atttctgggacttgaactcctgttatagaaggtcagattagccttaagctgaacagcagcagctacctgggcctttctcccctga ataaaagttctgaagatctaaaatgaaaatatgaaaggaaagaaattatcaagttctgtctactaaatatctcagtggatttcct acctcaactggtagatttgtcttaaggcctttgtttggagtgttttcctacaagtctcaaagtctaacaaaagcaggcgttcccg gtcaagctctgccaaattcaccacgtgacctaggacctgaagtgaactttcgtttctcctgttctctctctttccgaccttccct ccccgccaaggcaatgcagacagggactcaatatattattttgagttctccataggaaaagaattattattaaaacaataagctc tcaagataaatacctttatataatgtatatacattcatatatacatgagtatatactagctttcatatctgtattctatttttct ttctcacccagaactcaagaagacatgcctgtatcccttttttttttctcttttgagatgaagtttcactcttgttgcccaggct ggagcgcaatggcgcaatctcagcttactgtaacctccacctcctgcattcaagcaattctcctgcctcagcctcctgagtagct gggattacaggcgcccaccaccacgtctggctaatttgtgtatatttagtagaaatggggtttcaccatgttgaccaggctggtc ttgaacttctgacctcaggtgatccacccgcctcggcctcccagtgtgctgggattacaggcatgagccaccgcacccggcccaa catgtccgtattctcaaagctatagaggtgtctttgctattttgttctcttaggtaagaaccgggtcctcaccttacactttatt cctcaggtgaagagactctgtgtgtgtccattcagggaagcatgagagcatttgatttcagctgagcaggtttagtcatctagga gctgctctcttaagtgtttaacacaatcgttaactaactaaaacttgcaggaaattaatctggaatttcccagtaattacatgtt ttagataagtttttgaattgagtccaagatgatgtgatagtgcatgttcataattaactaagaaactgagaaaagctttcttaat ctaaaaacaaagccaaaaatctttccatgcaaggaaagaaaatcttaattgattaactcattaatagagcagggaaaagaaaaca aaagcaaaagcaaaaaaactaacttgagatatagctgaactcataatgtgtatttgtttttatttccagttgctgcttaccatta gctgtgcaagaccaaaggattttgtgctttctcttgcctagtaattgttcagtccaaaatttaaccatgttgtttttgtgttatt accaggagcaagaggacatgtgtattggtgagagaagaggggtgaggagtcagggataagatgaatctgattaacttcaggggtt attagaataaatcttgtaggcttggagaatcttgtaggcttggagaatctagagttctatgagaaatggtaagcagacttcataa atcctgtctgcgttgctgctatgatcttggccttcccctgacatactcccaagaaatagaaacgaatagaaatagaaatctaata gaactagaaatagaaatatttcccaagaaatagaaagtaaaactgacaaagccaatgcaaagaaatcagttcggaagctgttaat tttcacacgatctgtgttcagtaaccgccctctatcggctctcctgaatagcacactatatgggacggagaatctgaaaggcctt tttgctggttttcttactaacagagagttcataaaccaggatcttcttcagcctccaaggtaaggaaatgtgtgatctccaagct ccctcttgtatgtattgtgaacgccactgtcagaagagaaacaccaaagttattcacctggaaatgttgcagtatgaagaccatg tatttgatggagaggttatttaaatggtaactttgttaatgaatttctttgctaactttccctgctttattttcatgccaaaaac cagagaggtacagagaacagaactcggcaccacagtctaaaagtgttaagtttcaggcacaacactgctgtttttgagctgtggg tcctcagacaagccattttagctttccgagcctcagtttcccacttgcctgcttcttcaccacttcctggggtgataagagaaga ccaaatgatatgtttgtgaaggtgctttgccactcatgtaccctatgcagaccctattattagtagtactttataaaagtaagac atcattttctcatttacaggactgaggattagaaagaataatgctgggtttctggctgcctccgcttttgagggcctaggaggca ttctgacctaaagagagtaggcagtggagtcagacataaatgtaaacactgttagtgtgacctttgcagatcatctgtctgccct gtgcttctattatgctatctatctgcaaagtaaagaacttctttacaaaatgcctcatacaagtgtgaatacaacaaacaagctc catctctaaagttcttcatagaaaacagaattataagacgcactcagtatccaaggataaatgataccaggaaagggccaaagtt aattaatcctcttacaataaagagcatatttcaaggtaaataataaaaataattatcttaaaattaacaaaatgtatatggttat ttgcaactatgcattaattcttagcccaaagaatgttgaggagttgatttggcatgaagaggacacattttcttggacaaaatta taggatggcacagtgcgactttgtttagctcatactacctttcggtaacaccatcaaaggggatcttttttaccaaaaacatttt ttaaatcaagggttttcatcaattttccaaagggattaaaaaaattccctgacatttaagctggtacattttggaagcat SEQ ID NO: 2; LENGTH: 700; TYPE: DNA; ORGANISM: Homo sapiens catattgaatgcttagaacttgccaggccgtatctcagcacgtcactcatattaatcatttcctaataaccgctacaagttgggt tttgttattatccccatttgaataaataaggcacggagacacagagaggatatgacataactaccagaagccattggtggcaaga tctcaatcaggacatgtcggtacaatgctctgattatctcgtctgcatccctgattacttatggtccagatataaactactcctc ttcactttcattttaaccagaatttgaagtcattttattctctctcaagtactttgggctttgaggaaaataagggaaactcgcc acctggtggcagctcatagtgtgtggtaacaaggtggctgccccctgtctggtttcaaggagagaggagagaatgtccctgcctt gctattcacgcctctcaaacagctgagctgacctctcctcaagggccattgtctttagaaatccctcgccctgtctaggtccatt ctgataaaaattggagtagcagttttttctctatgcttcaagtgaggaggttggatgggacagagtccagcgatgagaggccaag actctcttgaccttatttcattgtcaaaaagatcagtattcatgttctacaagaaggaatccacagttgtccagaaaactgtcct tcaaaaatagccagtccaca SEQ ID NO: 3; LENGTH: 1720; TYPE: DNA; ORGANISM: Homo sapiens aagctctcagaggtatatgacagtctctccaccacagtgaccacatggagaggagaccattatctcctctcagtgagcccttgaa cccctgctccccaacaagtggagcctccaactcacaccagcagtgcagccacccacctcactggctgaacattcccagtaacagt gactctgcatttcttggggttggagccctcaggggcaaccaaaagcctctctgccactgcctctgtagtagtactacccctacta cctttagactaattaaacagcaaagaccctaagtgcctcatccacacccccaacaagctgcagttaacccaaggagaggagacc agtccatctcccacaggtcccatccacccctgctgcttgtcaccagggaaccccccagcttggacccacagtacagatcaccca tcttgggcctatcacactgagcaattgctgacctgcatctctgtggagtggagcccccaggagacaagtaaaagacccccagcca caaccactgctaaggtccttctctctgctgcctccaagctggggaggaaacataaaccctgagatctccccagagctgtggtgg gcagcctaggagtgccaagtctcaatctgtagccagcactcaaatgggagaggagtccacactttcagagcattgagaggtagc ccagctgcaaccatgaggaaatatagaggagtcacatgactgggaaagagtctacctactgaccactacttcacaaaacccctc atttccttctgtcctccctaaagcctctcagttttgaatctcatgtcttcaaattgtatcacccactggcctccatgaagcgcct aagcaccacctactggatcacaccccgcagcttcaacaccaaaaagttagaaagacttcaaattaacaacctaacatcacaacta aaagaactacagaaccaagagcaaaccaatcccaaagctagcagaagacaaaaaaacacatgcttatctcaacagatgtatctca ctaacatacccgccctgtaaaaccaaagataagaagtcagctgcaaataaagacctcgcacaaagcctcagccctgtgaaaatat tcaggaaaaaagtcttctgactgtactcaatctatgctgcagttaaaggaacacccatacacagagatgagaaagaaccaatgta agaactctggcaactcaaatgaccagtgtcttatgtactccaaacaatagcaccagttctccaatgagggttcttaaacaggctg agttggctgaaatgacagaaatagaattcagagtatagataggaatgaagatcattgagatttaggagaagaggaaaacacaatc caaggaaactaagaatcacaataaaatgataaaggagctgacaggcaaaatcgccagtattaaaaagaaacctaactgatctgat agagctgaaaagcacactgcaagaatttcacaatgcaatcgcaagtattaacagcagaatagaccaagctggggaaagaatctca gaacttgaagactggctctctgaaacaagacagccagacaaaaataaagaaaaaaagaatgaaaatgaatgaacagaaactccag aaaatataggattatgtaaggaggccaaatctataaatcactggcatcactgaaagagatggggagaaagcaaaccacttggaa aacacattttaggatatcactcatga SEQ ID NO: 4; LENGTH: 3660; TYPE: DNA; ORGANISM: Homo sapiens tctatttctattcgtttctatttcttgggagtatgtcaggggaaggccaagatcatagcagcaacgcagacaggatttatgaagt ctgcttaccatttctcatagaactctagattctccaagcctacaagattctccaagcctacaagatttattctaataacccctga agttaatcagattcatcttatccctgactcctcacccctcttctctcaccaatacacatgtcctcttgctcctggtaataacaca aaaacaacatggttaaattttggactgaacaattactaggcaagagaaagcacaaaatcctttggtcttgcacagctaatggtaa gcagcaactggaaataaaaacaaatacacattatgagttcagctatatctcaagttagttatttgcttttgcttttgattctttt ccctgctctattaatgagttaatcaattaagattttctttccttgcatggaaagatttttggctttgtttttagattaagaaagc ttttctcagtttcttagttaattatgaacatgcactatcacatcatcttggactcaattcaaaaacttatctaaaacatgtaatt actgggaaattccagattaatttcctgcaagttttagttagttaacgattgtgttaaacacttaagagagcagctcctagatgac taaacctgctcagctgaaatcaaatgctctcatgcttccctgaatggacacacacagagtctcttcacctgaggaataaagtgta aggtgaggacccggttcttacctaagagaacaaaatagcaaagacacctctatagctttgagaatacggacatgttgggccgggt gcggtggctcatgcctgtaatcccagcacactgggaggccgaggcgggtggatcacctgaggtcagaagttcaagaccagcctgg tcaacatggtgaaaccccatttctactaaatatacacaaattagccagacgtggtggtgggcgcctgtaatcccagctactcagg aggctgaggcaggagaattgcttgaatgcaggaggtggaggttacagtaagctgagattgcgccattgcgctccagcctgggcaa caagagtgaaacttcatctcaaaagagaaaaaaaaaagggatacaggcatgtcttcttgagttctgggtgagaaagaaaaaaaag aatacagatatgaaagctagtatatactcatgtatatatgaatgtatatacattatataaaggtatttatcttgagagcttattg ttttaataataattcttttcctatggagaactcaaaataatatattgagtccctgtctgcattgccttggcggggagggaaggtc ggaaagagagagaacaggagaaacgaaagttcacttcaggtcctaggtcacgtggtgaatttggcagagcttgaccgggaacgcc tgcttttgttagactttgagacttgtaggaaaacactccaaacaaaggccttaagacaaatctaccagttgaggtaggaaatcca ctgagatatttagtagacagaacttgataatttctttcctttcatattttcattttagatcttcagaacttttattcaggggaga aaggcccaggtagctgctgctgttcagcttaaggctaatctgaccttctataacaggagttcaagtcccagaaatccctagtcct ccatcagaggtaagtaaggatggcagctgaacccaagaaaaggagcatgaatgattaactcttccttcatttcacctcagaaaat gggggctgggcgcagtggctcacacctgtaatcccagcactttgggaggctgaggcagatggatcactgaggtcaggagtttgag accagcttggccaatgtggtgaaatcccatctctgctaaaaatacaaaaattagccaggcgtggtggcgtgtgcctgtaatccca gctacaccagaggctgaggcaggagaattgcttgaacccaggaggtggaggttgcagtgagctgagatcacgccattgcactcca gcctggacaacaagagtgaaactccatctcaaaaaaaaaaaaaaaaaaaaaaaggaaagaaagaaagaaaagaaaaataaaatgt ggggaaaaatattttactttaatactttgcctgccctgtcaagacgtagttcatcatgctttgtggggaaaaaattcacaattaa aaggatttagctctgtgtgacagctgatattcttaactgcaacggtctttctgaggagttattatttcaaagaaaaaagtgcatt gaggacaataaatatgtttattttcattggtaaagaaggaaagtagaataagttttcatatttgatttaagaatatgaattctac tctgttctttgcaatgattctatcttctagcaaacacattaaaagggcatttatttttcttacgctcaaccagaagcagctagtg tgtactgctctcacagagagaaatagatggggcgagtaaatactgcactttcaaccgaaacatacagatacacatgttggaattc atcaagaaaacaacctgacccatggagaatggagaaaagcagggcaggacaaccgcccacacgggagaaacatggagccagggga acctccccatccagggaagccgtgagtgaatgagcgaccctgcggaccaatgcttctcccatggatcgttgctactcttgggtca ggagatcccctcatgaacccactccactagggccttcagtcagatacacagagctatggggagtcttggcagagcagccgctcag gtacacacggagccccaggagccttagatatcctggcttcctggcaaaagtaactgctactccagccaagtgggaggttagaccc ccatacctactcctatgaaaggggctgaatccagggggctgagcagcgatgatctgcaggcctcacttccatagcacttcagagg tcacaggataagacccactggcttggaactctagccagctgctggtagcagcattacacatccctgagagggagctctcagagga aggggtaggcggccatctttgctgtttcacagcctcagtccttgttgccttcaggctttagagagtgcaaggtgatccatcagtg actggagtggaccccccagcacaacatggctgtcctgtggaaaagtggccagactgcttttttacacaagtctccaaacctgttt ctcctcactggatgagtcctcctggcctgggtctccacccaccccctgccagggatattgagccagtagcagctccataactctc tgggacagcgctcccagtgtttgggggttggggggtgagagggtggggggtgtgatgtttgctgtcttgcagcccttgcccttac tgtctccaggctctgaaaagtcctctgtgagtaccaggggctggtccagacccccagcacagagcgcccaccttagaaaagcggt cagactgttccccacaagtcccagtcctcactgcatagggctgcccgacctgagactccagcaccaccatcctgtttccgcctga ccacttcaatcagaggcacccccgcatttcttcgaagaggaaataaataccagagtgaacccacaaaccttcgcctctgcagttg c SEQ ID NO: 5; LENGTH: 4245; TYPE: DNA; ORGANISM: Homo sapiens ataaggctgcattcaggcataattaaatccaagtacttaaaagatgcagtcagaaatcaatctcctctctctctctgtctctcag tcttccactccatctcccacctccatgttgacctcattcttatgagacctctctccatgtggtaacatatgggtatcagcatctc tagactcacattctgccacttaagctatacttagaaacaataatcttctttctcagaaaaattcaagctgctacctcgattgata aactgcagccacttgtgcatggcttaaacaactttagtccattgtttccaaaattatatttgcatgtcactggtgctccctgaga tgatctggtagtaagcaaacatttattataatacatgccaggggctagaggggagggacggataaataggcagaacatggaggat atttagggaagtgaaattattccgatattatattggtgaatgcatgctgttttacatttgtcacatgtataattatgtgtaaatt tttatgcataataaaaaataagtagtgcctcaaaattattttcttttgcttgggatgaggctgaaataggaaggaaagtagtatt cattttacaggattagggtgagtttcagatatggtgatcaggcatgttcatgatcattttgtacctttacgaatcgaattatcaa acaagacttaacctgttccatgtagttgaagtgctgtacaggcagaaaaaatctagtcactgttgtatactgaggggaaaatctt aggttaagtccctcaaagattctggaaaaatttcatatggtaattcataaggcaatttttgaaaggaagtcaatatgtcacaaat tgaatgtaactttgaaaatctttaccctactttggaaaaaagtatcattttagtataacataaaatgaactacatgactgtcctc tccatggttaaattccttgtctgccaacattatataactgacttttgtttcttctgatttgttttcatgcagttaattttcaaga ggaagagcttccttcctaaatttgattcaaatctattccaggaacaaacagaagcttaaagtttcttttcacagtttcttttaag gcgccacttttgtttctctgtggtttcattatgagaagtaactcaaagtggaagaagattgttgtaatgtattgcatttctatac ttgagagagtttttaagttcttcagataagtatggtatgtggttgcaaggtaattttcacttatttgcaataatacaaatttgtg aatttctgttatttgttagctacacagtttatagtattttgttacagcaggcccaacagaataagagagacaataagcagattct gggaaaatggcagagtaggaagaaccaggaatctctctcctgacctacccaactaatgcagtggcagaatatgacttaactatct tggaactctggagtaatctaaggttcacaatttccagaggaaggcttaggttgtgtattagtttgttcttacgctgttatgaaga aatacctgagactggatgatttatgaaggaaagaggtttaattgacacacaattccacatgggtggggaggcctcaggaaactta taatcatggtagaagacaaaggggaagcgaggaccttcttcacatggtggcaagagagagaagagtgaaggaaaaacttccaaac acttataaaaccatcagatcttgcgagaactcactatcatgagaacagcatgggagaaactgcccccatgatccaatcacctccc tcccttgacatgtgatgattacaggtgcttccctcgaggtgtggggattacagtttgagatgagatttggtggggacacagagcc aaaccatatcattccacctctggcccctcccaaatctcatgtcttttcacatttcaaaaccgatcatgccttcccaacagtccct caaagtcttaactcatttcagcattaactcaaaagtccacagtccaaagtctcatctgagacaaggcaagtctcttccacctata agcctgtaaaattgaaagcaagttagttacttcctaaatacaatgggaggacaggccttgggtaaatgctcccattccaaatggg agaaattaaccaaaacaaaggggcgacaggccccatgcaagtctgaaatccagcaaggcagtccttaaatcttaaagctccaaaa tgatcttttttgactccatgtctcacacccaggacacactgatgcaaagagtgggctcccatggccttgagtagcttcttcacag gctggcattgagtgcctatggcttttttaggtgcacggtgcaagaaggaggtgaatctaccattcttgggtctggagaacagtga ccctcttctcacagctcccctaggcagtgccccagtggggactctgtgtgggggctcctaccccatatttcccttccacactgcc ctagcagaggttttccatgagggctctgcccctgtagcagacctctgcctggccatccaggcatttttatacctcctttgaaatc taggcagacattcccaaacctcaattcttgactaccatgtacccacaggcctaacactacagggaagctgccaaggtctggggct tgtaccctctgaagccacagcctgagctgtacattggctccttttagctatggctggagctaaagtggctgggatgcatcatacc aagtcccaaagctgcacacagcagtgggggcctgggcctggcccaataaatcatttttaacctcctaggcctccaggcctgtgat gggaggagctgccgccaagatctctgacaggctctggagatattttccccattgtctttgtgattaacattgggatcctcattac ttatgctaatttttgcagccagtttgaatttctccccagaaaatgggtttttcttttctactgcatggtcaggctgcaatttttc caaacttttatgctctgcttcccttttaaacgtaagttccaatttcaggtcatctctctcaagttcaaagttccacagaaatcta gggcaggggcaaaatgtcaccagtctctttgctaaagcatagcaagagtgacttttctccatttctcaataagttattaatctcc atctgagaccacctcagcctggacttcattgtccatccatatcattatcagcattttggtcaaaaccattcaacaagtctctagg aagttccaaactttcccacatcttcctgtcttcttctgagccctccaaattgttccaatctctaaccattacccagttccaaagt tgcttccacatttttttgtatttttgtagcagtaccccactaccttggtaccaattaactgtattagtctgttttcacactgcta taaagaagtacctgagactgggtaatgtataaaggaaaggggtttaattgaatcactgttccacatggctggggaggcctcagga agcttacaattatggcagaaggggaaacagccaccttcttcacaaggaagcaggagagagagcacacaggaaaaaactgccactt ttaaaaccagcagatgtcataagaactcactcattatcatgagaacagcatgggggaaaccacccccatgatccattcacctccc tcccttgacatgtgggaattacatgttcctccctcaacacaaatagggattataattcaagattcgatttgtctggggacacaga gccaaacaatatcaggttgtaaattgcagttagtttcagtcattgtcagctgtagccatcccttaccctcagcggcttggcaggc agctgtgcagatgatcctggagtagcttacacatagctttgcccagtgtggacaaaggaatgctgtactctaattattggggatc tgtgctctaaattgttgcttctaaacatagaagtacagaaaaaggaaaccactgttgcatgttctcttattgttgcccccctccc ccaccgaccccacttcccccaccctctagtgacttccaggaaatttgaaaggcaagtgctttttccccactttcatttttctcct ttcttttctggagggtcagacattaaggactaggacatttgaaattaagtcaccacataaacccggggaaaggggtacagactca gaaaacacttgagaagaccttacgtttgcacctcaggctaatgctcagcacacagatagcctacaaccaccccacaaaa SEQ ID NO: 6; LENGTH: 962; TYPE: DNA; ORGANISM: Homo sapiens Aacttatatttcctctttgcagctatgttttgggacttcctctttcacccatcaaaatatttctttaaaaaaaaaaatctttcct tccaagttttttcttcctttgttactatgacatgaataaatcaccttgtagattctctgtgttttgactgccttctcatggtcag ggactagaaagacctgttgtgtggccatttgctatggtctgccctaccctgacccctcagttcctacattgaagtcccaacctcc cagctgatggtagtaagaggtgggatcttttggagggtgactggatcatgatggccaagctcctgtgaatgggattagtgccctt ctaaaataggcccaagggagctcattcacctcttgtcacctcttttcacctcttccaccatgcaaagacacagcaagaagatgct gtctttgaaccaggaaagctagccctcacagacaccaagtctgccttgatcttaaactttccaggccctggaactgtgagaagta aatttctgtggtttataaaccacccagtttaagatattttgttgtagaaaccccaacagactaagtcagcaatgcaaaaaatatt agaactaaagggaccttgcactaatctcatataagcccttcatttttaaatatgaaaacaaaacaaaaccgaagtcctggcaatt agcctactaaatccacaggtagccagaggtagaactgactcattgttatgtctccccagctcaaacgtgttcttccagatcataa acattggcttatgcttctttccatctcctttaaaccccagacaactgctgggcacatgtaatactttaaaaatatttctatatcg gccaggcatgatggctcatgcctgtaatcccagcactttgggaggccgaggtgggtgcattacctgaggtcaggagtttgagacc agcctgagtaatatggtgaaacaccgt

Targeting TNFSF10 eRNA activity limits cell apoptosis. Thus far, the inventor has identified a highly validated set of functional eRNAs and established that modulation of these eRNAs can yield selective changes in target gene expression. These findings may be valuable for a therapeutic intervention by targeted enhancement or reduction of disease-relevant genes. In the context of the anti-viral response in human and mouse, overexpression of the TNFSF10 gene has been implicated in inducing lung damage by influenza virus (Hogner et al., 2013). The inventor reasoned that by targeted reduction of TNFSF10 eRNAs to decrease TNFSF10 expression, he may be able to limit apoptosis without affecting interferon production or response. In order to examine the possibility of eRNA modulation for reducing apoptosis, the inventor performed siRNA-mediated reduction of TNFSF10 eRNAs and checked cell viability (FIG. 6A). TNFSF10 expression level, upon triple eRNA KD, decreased about 50%, compared to control (FIG. 6B). Control cells showed a stronger signal for cleaved Caspase 3 than the TNFSF10 eRNA KD cells and a positive control, IFNB1 eRNA KD cells (FIG. 6C). Furthermore, reduction of TNFSF10 eRNA resulted in a higher proportion of live cells and a corresponding decrease in apoptotic cells (FIG. 6D). To confirm TNFSF10 eRNA KD is specific for limiting the viral induced apoptosis, the inventor induced TNFSF10 expression by a distinct mechanism using TIC10, a small molecule inducer of Foxo3a that activates the TNFSF10 promoter (Jacob et al., 2014). Thus, TIC10 treatment would result in apoptosis via a distinct mechanism, compared to viral infection induced apoptosis. As expected, TNFSF10 eRNAs KD, either individual KD or triple KD, did not affect TIC10-induced apoptosis (FIG. 6E; FIG. 13 ). In addition, TIC10 treatment induced TNFSF10 expression significantly, but it did not affect expression of the virus inducible eRNAs associated with the TNFSF10 gene (FIG. 6F, Left). In contrast, virus infection induced expression of those eRNAs as well as the TNFSF10 gene (FIG. 6F, Right). Taken together, these results demonstrate that targeted reduction of eRNAs can specifically inhibit interferon induced apoptosis.

Example 2—Discussion

Regulatory genomic elements outnumber genes by two orders of magnitude. More than two million enhancers have been annotated in the human genome (Romanoski et al., 2015). One fundamental question is whether all these enhancers are functionally equivalent or whether there are distinct classes of enhancers that are more relevant in different conditions. To explore the landscape of potentially functional enhancers and associated eRNAs, the inventor used the virus inducible gene expression model. He identified potentially functional eRNAs by taking advantage of the dynamic expression information from global transcriptional analysis and using associated genomic proximity and transcriptional activity as criteria. Specifically, the inventor considered inducibility of enhancers upon virus infection and applied this activity-based association strategy to identify their target gene. From this strategy, he was able to assign 123 eRNAs to their most likely target genes. Using these highly confident EP pairs, the inventor tested the functionality of eRNAs at both physical interaction level and biochemical level. More than 80% of the inducible EP pairs showed a higher physical interaction frequency at 12 hours—a time point representing the peak of transcription level. In addition, reduction of eRNA levels by RNAi decreased target gene transcription for all inducible eRNAs tested. From these results, the inventor concludes that the virus inducible eRNAs are indeed functional. The control pairs for the inventor's experiments were selected by general criteria that other groups have routinely used for determining active enhancers. The inventor's 3C results and targeted eRNA reduction results from control sets might explain why many groups have argued that eRNAs are dispensable for enhancer function. Thus, co-inducibility of eRNAs and genes would be relevant for identifying other functional eRNAs in different biological conditions.

One unexpected finding from this study is that the fate of an enhancer can be different from the promoter it regulates after their transient functional and physical association. In many independent cases, eRNA production continues while the enhancer becomes disengaged from its associated promoter and the target gene undergoes post-induction repression. In other cases that conform to the current paradigm of gene regulation, when an enhancer disengages from its promoter, both eRNA and mRNA production are shut off concordantly. Furthermore, dependence of eRNAs for physical interaction between enhancers and promoters does not seem to be a universal mechanism across different loci (Li et al., 2013; Schaukowitch et al., 2014). Rather, each locus exhibits different dependencies on eRNAs for enhancer-promoter interaction. Notably, some loci display competition among enhancers and promoters when assayed for physical interaction. In reduced-function assays using RNAi, enhancers within the same locus can also compete for production of corresponding eRNAs. Despite the complex regulatory dependencies among enhancers and promoters, a combined reduction of all eRNAs for a given target gene resulted in the largest decrease in target gene expression compared to individual eRNA knockdowns, suggesting a complete pool of functionally relevant eRNAs is necessary for proper regulation. Thus, the human genome displays dynamic and complex exchanges of physical and functional associations among enhancers and promoters to define genome expression. Intriguingly, these functional properties of eRNAs are consistent with a recently proposed model of RNA-mediated phase separation for gene regulation (Hnisz et al., 2017).

Lastly, the inventor demonstrated that he can modulate one particular enhancer of the anti-viral program to achieve a specifically modified cellular behavior that can aid in reducing excessive inflammation. With hundreds of functional eRNAs identified in this study, targeted therapies with tailored modulation of multiple enhancers may be an approach to achieve a personalized clinical response.

Example 3—Methods

Cell culture and virus infection. B-Lymphocyte, GM12878 cells, were obtained from Coriell Institute for Medical Research and cultivated according to the supplier's instructions. 15% fetal bovine serum was added to Roswell Park Memorial Institute media 1640 (RPMI-1640) with 2 mM L-glutamine for the culture. Sendai Virus (Cantrell strain) obtained from Charles River was infected for inducing immune response signaling gene expression system, of which 50 μL was added to 1 mL media. Cell samples were taken at 30 min, 1 h, 2 h, 4 h, 6 h, 12 h, 18 h, 24 h, 48 h, and 72 h after virus infection for GRO-seq experiment. For the other experiments, 3C assay and ChIP-seq experiment, the cells incubated for 6 h, 12 h, 18 h, and 24 h after infection were sampled. Untreated GM12878 cells were used as a control, which is 0 h sample.

GRO-seq analysis. Global run-on and library preparation for sequencing was performed based on the method published by John Lis et al. in 2008 (Core et al., 2008). Some parts of the protocol were modified to accommodate the inventor's experimental purposes and multiplexing (Kim et al., 2013).

Nuclei isolation. Two 15-cm plates of confluent cells (˜10-20 million cells) were washed 3 times with ice cold PBS buffer and incubated for 5 min with 10 mL cold swelling buffer (10 mM Tris-Cl pH 7.5, 2 mM MgCl₂, 3 mM CaCl₂)) for each plate on ice. Cells were scraped from the plate, harvested, centrifuged at 500×g for 10 min at 4° C., and were resuspended in 1 mL of lysis buffer (swelling buffer with 0.5% IGEPAL, 10% glycerol and 4 U/mL SUPERaseIn) with gentle mixing by pipetting with a widened boar pipette tip up and down 20 times. For the isolation of nuclei, 9 mL of the same lysis buffer (up to total 10 mL) was added. After collecting the nuclei by centrifugation (at 300×g for 5 min at 4° C.), it was resuspended in 1 mL freezing buffer per 5 million nuclei, and pelleted and resuspended to the final volume of 100 μL (about 5-10 million nuclei/100 μL) of freezing buffer (50 mM Tris pH 8.3, 5 mM MgC₂, 0.1 mM EDTA, 40% glycerol).

Nuclear Run-On (NRO). Before the NRO reaction, NRO reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl₂, 1 mM DTT, 300 mM KCl, 50 M ATP, GTP and Br-UTP, 2 μM CTP, 0.4 U/μL RNasin, and 2% sarkosyl) was generated and pre-heated to 30° C. for 5 min. An equal volume (100 μL) of NRO reaction buffer was mixed with 100 μL of thawed nuclei solution in freezing buffer and was incubated at 30° C. for 5 min with mixing at 800 rpm on a thermomixer. Then, RQ1 DNaseI (Promega) was added along with DNaseI reaction buffer and samples were incubated at 37° C. for 20 min with mixing 800 rpm. To stop the NRO reaction, 225 μL NRO stop solution was added to the reaction and 25 μL of Proteinase K was added. The sample was incubated for 1 hr at 55° C. Nuclear RNA was extracted with acidic phenol (Sigma) then with chloroform (Sigma) and was precipitated and washed. RNA was then resuspended in 20 μL of nuclease free water and subjected to base hydrolysis by addition of 5 μL of 1N NaOH on ice for 10 min. The reaction was neutralized with 50 μL of 0.5 M Tris-Cl pH 6.8. Then, RNA was purified through BioRad P-30 RNase-free spin column (BioRad) following to the manufacturer's instructions and was treated with 7 μL of DNaseI buffer and 3 μL RQ1 DNaseI (Promega) for 10 min at 37° C., and purified again with a BioRad P-30 column.

Anti-BrU agarose beads (Santa Cruz Biotech) were equilibrated by washing them 2 times in 500 μL BrU binding Buffer (0.25×SSPE, 1 mM EDTA, 0.05% Tween-20, 37.5 mM NaCl) and blocked in 1 mL BrU blocking buffer (1× binding buffer, 0.1% PVP, and 1 mg/mL BSA) for 1 hr with rotation at 4° C. During the blocking step, beads were washed 2 times with 500 μL binding buffer, NRO RNA sample was heated at 65° C. for 5 min then placed on ice at least for 2 min. 50 μL of the blocked bead mixture was combined with RNA sample in 450 μL binding buffer and combined with bind RNA to beads for 1 hr by rotating at 4° C. After binding, beads were washed once in low salt buffer (0.2×SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.25×SSPE, 1 mM EDTA, 0.05% Tween-20, 137.5 mM NaCl), and twice in TET buffer (TE with 0.05% Tween-20). BrU-incorporated RNA was eluted 4 times with 100 μL elution buffer (20 mM DTT, 300 mM NaCl, 5 mM Tris-Cl pH 7.5, 1 mM EDTA and 0.1% SDS). RNA was then extracted and precipitated as described above. The precipitated RNA was re-suspended in 20 μL of water.

TAP/PNK treatment. RNA was heated to 65° C. for 5 min and cooled on ice at least for 2 min. The RNA was treated with TAP (by adding 3 μL 10× TAP buffer, 5 μL water, 1 μL SUPERaseIn (Promega), 0.5 μL TAP) at 37 for 1.5 hr, and then preincubated with PNK reaction premix (1 μL PNK (NEB), 1 μL 300 mM MgCl₂, 1 μL 100 mM ATP) for 30 min. Afterward, PNK reaction main mix (20 μL PNK buffer (NEB), 2 μL 100 mM ATP (Roche), and 142 μL water, 1 μL SUPERaseIN (Promega) and another 2 μL PNK (NEB)) was added to the preincubated RNA sample and incubated at 37° C. for 30 min. The RNA was extracted and precipitated again as above and resuspended in 9 μL water.

5′-adaptor ligation. BrU-RNA, 5′ adaptor (5 uM) and PEG was heated on 65° C. for 5 min then cooled on ice. Ligation mixture (1.5 μL 5′ adaptor (5 uM), 2 uL 10× RNA ligation buffer, 1.5 uL T4 RNA ligase, 1 uL SUPERaseIn, 5 uL 50% PEG 8000) was added to the 9 uL BrU-RNA and incubated at 22° C. or RT for 4-6 hours. Then, 5′ adaptor ligated BrU-RNA was purified with the bead binding method as described above.

3′-adaptor ligation. The same ligation reaction for the 5′-adaptor ligation described above was performed with the 3′ adaptor in place of the 5′ adaptor.

RT-reaction. RNA and RT oligo (5′-CAAGCAGAAGACGGCATACGA-3′(SEQ ID NO: 644)) was heated to 65° C. for 10 min and cooled on ice. RT reagent mixture (1 μL RT oligo (100 μM), 5× first strand buffer (Invitrogen), 10 mM dNTPs (Roche), 100 mM DTT (Invitrogen), 1 μL RNase inhibitor (Promega) without Superscript III (Invitrogen) was added to RNA sample and incubated at 48° C. for 3 min, and then 1 μL superscript III was added to the RT reaction sample and incubated at 48° C. for 20 min, 50° C. for 45 min, sequentially. After RT reaction, RNA was eliminated by adding RNase cocktail and RNaseH and incubating at 37° C. for 30 min.

PCR amplification. The ssDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer's instructions. The small RNA PCR primers (5′-CAAGCAGAAGACGGCATACGA-3′(SEQ ID NO: 644)) and (5′AATGATACGGCGACCACCGACAGGTT-3′(SEQ ID NO: 645)) were used to generate DNA for sequencing. PCR was performed with an initial 5 min denaturation at 98° C., followed by 10˜14 cycles of 10 sec denaturation at 98° C., 30 sec annealing at 54° C., and 15 sec extension at 72° C. The PCR product was purified by run on a 6% native polyacrylamide TBE gel and recovered by cutting the region of the gel between 100 bp to 300 bp. The product was purified through the gel extraction method. The prepared DNA was then sequenced on the Illumina Genome Analyzer II according to the manufacturer's instructions with small RNA sequencing primer 5′-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3′ (SEQ ID NO: 646).

eRNA annotation. The inventor first merged GRO-seq data across time points and used HOMER (Heinz et al., 2010) for de novo transcript identification with option ‘-style groseq’. Intergenic transcripts, which were >1 Kb from 5′ ends and >10 Kb from 3′ ends of RefSeq gene annotations, were selected as eRNA candidates. The RefSeq annotation was downloaded through an R package called “GenomicFeatures” (Lawrence et al., 2013), with “GenomicFeature” version 1.20.3 and creation time “2015-11-24 13:48:33-0600 (Tue, 24 Nov. 2015)”. The inventor filtered out regions that did not overlap with either H3K4me1 or H3K27Ac peak regions.

ENCODE epigenetic data analyzed here can be downloaded from GEO under accession numbers GSE29611 (H3K4me1 and H3K27Ac), GSE29692 (DNase-seq), GSE35586 (MNase-seq), and GSE31477 (P300). Human enhancer atlas data were downloaded from (slidebase.binf.ku.dk/human_enhancers/, the permissive enhancer set).

Expression analysis of coding and non-coding transcription. Expression levels of genes and enhancers were calculated as Reads per Kilobase per Million (RPKM). R package DEseq2 (Love et al., 2014) was used to perform differential analysis between two time points. Differential gene sets were submitted to David Bioinformatics Resources Database (Huang da et al., 2009a, b) for functional enrichment analysis. Principle Component Analysis (PCA) and t-Distributed Stochastic Neighbor Embedding (t-SNE) methods were applied with expressed genes/enhancers (mean RPKM>0.5) for data visualization.

The inventor designed one-step delayed auto-correlation to control noise levels and the absolute fold-change to identify responsive genes/enhancers. Selected genes/enhancers were subject for clustering by the ‘Partitioning Around Medoids’ (PAM) algorithm, resulting in three clusters: “inducible early,” “inducible late,” and “repressed.”

Determining inducible enhancers and genes. The inventor identified inducible enhancers/genes using the amplitude index (AI) and continuity index (CI). The expression level at time t is represented as e(t). AI is defined as the maximum logarithm fold increases before 24 h:

${AI} = {{log2}\left\lbrack \frac{\max\limits_{t \leq {24h}}{e(t)}}{e(0)} \right\rbrack}$ CI is defined as the one-step delayed auto-correlation, to filter out enhancers/genes with noisy expression pattern: CI=correlation{[e(t ₁), . . . ,e(t _(n−1))],[e(t ₂), . . . ,e(t _(n))]} The inventor then selected enhancers and genes with AI>1 and CI>0.2 as inducible.

Concordant and discordant EP pairs. Inducible EP pairs were ranked by the Spearman correlation coefficients (SCC) between enhancers and genes. Pairs ranked at the top 30% and bottom 30% of the list are designated as concordant and discordant, respectively.

Pairing enhancer and target genes. Fold changes at each time point were calculated for enhancers near inducible genes. The inventor divided enhancers into groups according to their distance from genes and found enhancers <200 Kb from these genes showed significantly stronger inducibility. He named inducible genes and enhancers within 200 Kb distance as inducible EP pairs.

Motif analysis. The inventor used TF binding motif PWM matrices from HOmo sapiens COmprehensive MOdel COllection (HOCOMOCO) v10 (Kulakovskiy et al., 2016). The inventor applied HOMER module annotatePeaks.pl to identify motif occurrence in inducible enhancers and genes.

Synteny analysis. The inventor analyzed EP co-localization in 11 species covering different levels of metazoan animals, including chimp, marmoset, mouse, rat, guinea pig, rabbit, cow, dog, elephant, armadillo, and lizard. Orthologs of enhancers and promoters were identified using UCSC LiftOver tool with minimal match ratio set to 0.1. The inventor tested the percentage of inducible human EP pairs locating in the same chromosome in other species. For statistical analysis, the inventor generated a background set by paring 10,000 random promoter regions with the same number of intergenic regions, following the distance distribution of inducible pairs.

Chromatin Immunoprecipitation (ChIP) sequencing. Chromatin was prepared and immunoprecipitated as described previously (Kim et al., 2011), except that protein A/G dynabeads (Invitrogen) were used instead of organism-specific secondary antibody bound beads. 25% of the amount of chromatin was used to reduce oversaturation of bead binding. K27Ac antibody from Abcam (ab4729) was used for ChIP experiment. The ThruPLEX DNA-seq kit from Rubicon Genomics was used for multiplexed ChIP-seq and Input sample library prep of GM12878 chromatin. Indexed samples were quantitated with qPCR and mixed in equimolar amounts. The Yale Stem Cell Center Genomics and Bioinformatics Core Facility conducted the sequencing on an Illumina HiSeq 2000 platform. ChIP-seq peaks were called with MACS 2 with the default mode. The inventor analyzed the inventor's ChIP-seq data using the inventor's scripts and tools.

Chromosome Conformation Capture (3C). The 3C assay was performed as described (Banerjee et al., 2014; Kim et al., 2011), with minor modifications. Briefly, one million cells were cross-linked with 1% formaldehyde for 15 min at room temperature, and resuspended in lysis buffer (10 mM Tris, pH 8.0, 10 mM NaCl, and 0.2% NP40) and incubated on ice for 90 min. Ten million of these prepared nuclei were digested with EcoRI (New England Biolabs) overnight at 37° C., followed by ligation with T4 DNA ligase (New England Biolabs) at 16° C. for 4 hrs. The ligated DNA was incubated with Proteinase K at 65° C. for 12 hrs to reverse the cross-links. Following incubation, the DNA was treated with RNase A. The treated DNA was extracted with phenol:chloroform and precipitated with sodium acetate and ethanol. The DNA concentration of the recovered 3C library was determined using Qubit dsDNA HS assay kit (Invitrogen). Quantitative real-time PCR was performed to confirm the specific ligation between two DNA fragments in the sample and control 3C libraries. The position and sequence of primers designed for 3C qPCR assay is listed in Supplemental Table S4. Interaction frequencies were calculated by dividing the amount of PCR product obtained with the sample 3C library constructed from nuclei by the amount of PCR product obtained with the control library DNA generated from ligating EcoRI fragments from the corresponding bacterial artificial clones (BAC, Supplemental Table S4): interaction frequency=2{circumflex over ( )}(dCt sample−dCt control). All 3C analyses were performed, at a minimum, in triplicate.

TABLE S4 3C assay primers and BAC clone for induced EP interaction (a) and control EP interaction (b). Target genes Control eRNA SEQ Target Target SEQ Target SEQ SEQ Enhancer eRNA- ID gene promoter- ID promoter- ID Control ID ID primer NO: name primer1 NO: Primer2 NO: primer NO: BAC done A. Induced EP interaction MetaEnhancer_ TCACGAACACC 7 ACKR1 AACTCTGATGG 43 TTGGTCACCC 79 TCCGTAGTGAA 115 RP11-621D16 + 1136_+ CAGAGATGT CCTCCTCTG TTTCTCCAGG AGTTTTGGGA RP11-1065J8 MetaEnhancer_ ACCACCAGACA 8 CCR1 GGAGGGCAGT 44 CTTCCTCACG 80 CTGCTCTTGT 116 RP11-793E15 258_− TTAGCCCAG GTTGTTCAAA GCATTGCTAC TCTCCACTGC MetaEnhancer_ TGCTGCCACAA 9 CD38-1 TCCTGTTGTGT 45 GGAGTCCAAA 81 TGATCCTTTC 117 RP11-640L4 1694_+ GAACATTTG ACCTGGCTT GGCAGTCTCT CTTGGCCTCA MetaEnhancer_ GTGTGTGTGTG 10 CD38-2 GGAGACCCAG 46 TCCTGTTGTG 82 ATTACAGCAC 118 RP11-640L4 3795_− TGTGTGTGT GGAAGAGTTG TACCTGGCTT TTTGGGAGGC MetaEnhancer_ TCACGAACACC 11 IFI16 GCAGTGATCAAA 47 TCCAAGGCCA 83 GTGCTGTCTC 119 RP11-265E4 1136_+ CAGAGATGT ATTATGTCCCA TCTACAGAGC CCTTCTGTCT MetaEnhancer_ TCCCCAGTCAT 12 IFNb1 GCAAAGGAAA 48 TCCCCACTGC 84 TCAGGTAATGT 120 RP11-372B20 1571_+ TAGCACAGT GCAAACGACC CTTGTTCATA GATGCCTCCA MetaEnhancer_ ATAGCCTGCCC 13 IRF8 GAAGTGCTCTG 49 TGGGCATTTG 85 TGTTAATTAC 121 RP11-478M13 + 259_+ CAAATCACT CTTTCCGAG GTGGAATTCg CTGAAGCGCGT RP11-152O13 MetaEnhancer_ TCTTGGGACCG 14 KIAA0040 ATCCAAGTGTT 50 CTTTCTCCGA 86 AAAGAAAATGC 122 RP11-661N21 1115_+ TGAAAGTGT TCCAACCGC ACGCTCAAGG CAGGCCCAG MetaEnhancer_ TCACGAACACC 15 MNDA CAAATCAACG 51 ATCATGAGAA 87 TGAGTTGGCTG 123 RP11-110D10 + 1136_+ CAGAGATGT GGAGCAAGCT CAGCACGGGA TAAATGTGTGT RP11-1065J8 MetaEnhancer_ TGGTTGGACA 16 PARP14 TCATATCTCTC 52 TCTTGGTCCA 88 GGGTCAAAGAG 124 RP11-90P23 2972_− GTAGGGGAAG TGGCTGCTCC ATGCAGTCCT ATGGCAGGA MetaEnhancer_ TGGTTGGACA 17 PARP9 ATCTCTTGGCC 53 TGAGGACCCT 89 TTACAGGCACG 125 RP11-90P23 2972_− GTAGGGGAAG ATGGAGCTT ACTGTTGCTG TACCACCAT MetaEnhancer_ AGCATTTAGGA 18 SAMD9 GATGTTAGGG 54 TGAGCACTTT 90 TTTGCTGTAAC 126 RP11-962H11 3039_+ GTGCACGTT GCTCTGCAGA GGAAGGCAAG TGCCCTCCT MetaEnhancer_ CTGTCCCACAC 19 TLR7-1 CAGGAAGAGG 55 GAGGGTTTCAT 91 GTAAACCACTG 127 RP11-166I19 502_+ ACCCCATAT GAGAGCAGAG TTGCTGGGG CAGACTGGC MetaEnhancer_ CTGTCCCACAC 20 TLR7-2 CAGGAAGAGG 56 GAGGGTTTCAT 92 CATGCCAAGAT 128 RP11-166I19 341_− ACCCCATAT GAGAGCAGAG TTGCTGGGG CTGTAGACATC T MetaEnhancer_ TCTCCATGGGT 21 TNFSF10-1 TACAGGTTCT 57 GAGCTGAGAT 93 GCCATGCGCGG 129 RP11-240B20 116_+ CAGGTTGTT TTGGTGCCCA CATGCACTGC GATATAATC MetaEnhancer_ CTCCATGTTTC 22 TNFSF10-2 TACAGGTTCT 58 GAGCTGAGAT 94 GAGGACTACAG 130 RP11-183A2 734_− TCCCGTGTG TTGGTGCCCA CATGCACTGC TAACGACCCT MetaEnhancer_ GCAATAAACGT 23 TNFSF10-3 GAGCAGGACA 59 TGCCCATTTTC 95 ACATTGTGCCC 131 RP11-259F22 2005_+ GGGAATGCC CGTAGACTCA AGCATACAAAA AGATGTTCC MetaEnhancer_ CACAGAAAGC 24 WDFY1 AGGCTGGTCT 60 TGTAGGAGGA 96 CTGGCAGACAC 132 RP11-79C2 512_− ATTGCCCCTT TGAACTCCAA GCAGGTTTGG CTCCACTTA B. Control EP interaction MetaEnhancer_ CTGGTCTTCTC 25 APOBEC3B GCCTCAGCCT 61 CCTAGGGTAG 97 GGGATTACAG 133 RP11-358G23 600_+ TTCCCCACT CTAGAGTAGC CCTCACGTG GTGCCCAGAA MetaEnhancer_ CTGGTCTTCTC 26 APOBEC3D- ACTCCCAACC 62 CACCTCTCTG 98 GGGATTACAG 134 RP11-358G23 600_+ TTCCCCACT 1 TCATGATCCG TGCCTCTGAC GTGCCCAGAA MetaEnhancer_ CTGCTGGTCTT 27 APOBEC3D- TCGAACTCCC 63 CACCTCTCTG 99 ACAGAGTTCA 135 RP11-358G23 94_− CTCTTCCCC 2 AACCTCATGA TGCCTCTGAC GGACAGTGGT ACAATCAGTCA MetaEnhancer_ CTAGGAGGAG 28 CD2AP AAGGATTGGG 64 GTATGTGTGG 100 TGGTAGGAGC 136 RP11-947C14 1529_+ G GAGTCTCTCG GCATTTGTGC CCAGATTCTG MetaEnhancer_ CCATGTTTGCT 29 DMXL1-1 ATCCCTGCGG 65 CTGCATGCCAA 101 CCCTGCTGCT 137 RP11-119J15 699_+ AGGCTGGTC CCGAAATAT ACTTAAAACCT TCCCTTTGAA MetaEnhancer_ CCATGTTTGCT 30 DMXL1-2 TCCACACACT 66 AGAAAGGTGT 102 ATCCACAGAAC 138 RP11-119J15 454_− AGGCTGGTC TCCTCTGGAC TTGTGGTGCA CATGCTCCA MetaEnhancer_ CACTTCTCATT 31 HLA-DMA GGCCGAAGTA 67 CAAGCTACTC 103 GACCCAGGAAG 139 RP11-260B12 475_+ TCTCCAACCAC CCTAGCATGT AGGAGGCTGA AGCTGATGT A MetaEnhancer_ TCCAAACATGC 32 HLA-DRA TCCAAAGGCA 68 TCTGCTCAGG 104 CTGAAGAGTGA 140 RP11-379F19 157_− AGCAGTCAC CCTGAATGAG AATCCTAGGT cAcacacA MetaEnhancer_ TCACCACCTTC 33 HLA-DRB5 ATTCCCCATAC 69 TTGCTTCTCTG 105 CTGAAGAGTGA 141 RP11-379F19 157_− CGGACTTTT AGCACTTCC TTTTCTTTCCC CACCTCCTCA MetaEnhancer_ CCAAAAGCAC 34 IFI35 GAGAGAGACC 70 AAACTCTCCC 106 CCAGCCCCTTA 142 RP11-948G15 820_− AAGACAGCCT ACAGCCCTTT ACGTTCACCC TGCCTCTTA MetaEnhancer_ CTGTGGGTCAA 35 MLLT6 TATTCCAGGGC 71 CATCTCCCTC 107 CAGCTTGAAGT 143 RP11-607B2 311_+ ATGGGAGGA CTAGAACGG TTGGCTTCCA GCCTTGTGG MetaEnhancer_ AGGGACAAGC 36 MYCBP2 GAAGGGGTGG 72 CTCCTTCAGC 108 TTTCATGGCTC 144 RP11-775N1 544_− AAGCATCTCT AGGTGAGTAC CACTTCAGGA CAACAACCT MetaEnhancer_ AACTTGAGCCC 37 PELI1 CGATGCGTTTT 73 GCCCGGCCAA 109 CACTTCTGGTT 145 RP11-46K17 327_+ AGACAACCT CTTTATAGCCA ATATCAGTAG TCTCATTCTCG A MetaEnhancer_ GCTTGCCTCTC 38 SOCS1-1 GCGGTCTTAT 74 AGTCAAGATC 110 CTCTGCCCAGC 146 RP11-697G17 1477_− TTTGCCTTA GTGGTATGCC CTGGTGGCTT CTAGGAAC MetaEnhancer_ CCTTGGTTTCC 39 SOCS1-2 AGTCAAGATC 75 GCGGTCTTAT 111 CAGGAGGCTCT 147 RP11-697G17 810_− TGGCCTCTA CTGGTGGCTT GTGGTATGCC GGGAAGAAT MetaEnhancer_ TGCATGAGGC 40 ZBP1 CCCAAGTCTC 76 GTGTGAAGTC 112 AACGGGAGCTT 148 RP11-1105M4 + 1228_+ AGACTTGTTC CCTTCTACCA AGGTGCATGG CGACTGTAA RP11-877E5 MetaEnhancer_ TGTGGTCCATA 41 ZCCHC2 CCAGGCTGGC 77 CCACTCTTCAG 113 CAAGTCCTGCC 149 RP11-645G19 804_+ TCCCGTAGA AAATTGAGTT CCTACTCGT CTGGTTTAC MetaEnhancer_ CACGCCCAGCT 42 ZFAND6 GCGGAGACTT 78 TTAAACATTTTA 114 GAACAAAAGCT 150 RP11-916P11 246_+ AATGTTTGT TAAGGGCTTG GCATCCCCAGG CCTGAGGCC

eRNA KD analysis with siRNA. siRNA duplex for eRNA KD were obtained from Sigma-Aldrich. Their sequences and eRNA region of induced EP pairs and control EP pairs are listed in Table S5 and Table S6, respectively. As a negative control, scrambled siRNA was used. As a mock control, only transfection reagent without siRNA was added to cell sample. 300,000 cells were prepared in 800 μL media in each well of 12 well-plate. Separately, siRNA transfection solution was prepared by adding 1 μL of siRNA (10 uM stock of siRNA) and 5 μL of Mission siRNA transfection reagent (Sigma) to 200 μL OPTI-MEM, followed by incubation for 15-20 min at room temperature. Then, siRNA transfection solution was added to the cell carefully, by dropping it, which was incubated for 5 hours at 37° C. and then changed with fresh media. After 36 hours of incubation, virus solution with the concentration of 50 μL/mL media was added to the cell to activate the inducible immune response gene system. After 12 hours, total RNA was extracted with adding 500 ul of Trizol solution (Invitrogen) to the cell pellet spun down at 1,500 rpm for 3 min and rotating at 4° C. for 5 min.

TABLE S5 siRNAs targeting eRNA of induced EP pairs.  SEQ siRNA  SEQ Sequence SEQ Sequence SEQ  SiRNA target ID SiRNA sequence ID (Sense) ID (Antisense) ID  name gene Items eRNA region NO: name Position NO: 5′ to 3′ NO: 5′ to 3′ NO:  siRNA# TNFSF MetaEnhancer_ TAAACCAGGATCTTCTTCAGCCTCCA 151 116A GCCACTGTCAG 170 GCCACUGUCAGA 213 UUUCUCUUCUGA 256  5A 10-1 116_+ AGGTAAGGAAATGTGTGATCTCCAA AAGAGAAA AGAGAAA CAGUGGC SiRNA# GCTCCCTCTTGTATGTATTGTGAACGC 116B TCTTCAGCCTCC 171 UCUUCAGCCUCC 214 UUACCUUGGAGG 257  5B CACTGTCAGAAGAGAAACACCAAAG AAGGTAA AAGGUAA CUGAAGA SiRNA# TTATTCACCTGGAAATGTTGCAGTAT 116C GGAAATGTGTG 172 GGAAAUGUGUG 215 UUGGAGAUCACA 258  5C GAAGACCATGTATTTGATGGAGAGG ATCTCCAA AUCUCCAA CAUUUCC SiRNA# IRF8 MetaEnhancer_ GGCTCAGGCTGAGAGGATATTCTGCC 152 259A GAGAGGATATT 173 GAGAGGAUAUU 216 AACGGCAGAAUAU 259  7A 259_+ GTTGTAGTTTTGCTCGGGGCCATTCG CTGCCGTT CUGCCGUU CCUCUC SiRNA# TTTTAAGAAGACTGGAGAGTCAGTTC 259B GGTTTCTACTGG 174 GGUUUCUACUG 217 UAAGCCACCAGUA 260  7B CAGTTTGTCTTGGGGGACTAAGTTCT TGGCTTA GUGGCUUA GAAACC TATCATGTGGTTTCTACTGGTGGCTTA TTAGAACACATGCAGGTACAG SiRNA# MLLT6 MetaEnhancer_ CCCAGCCCTCAGTGGCCCCACAGCAG 153 311A CTCTGCTTCTGC 175 CUCUGCUUCUGC 218 AUAUCAUGCAGA 261  8A 311_+ CTTGGCTGTTCTTGGTTTTGTTTCTCT ATGATAT AUGAUAU AGCAGAG SiRNA# CTGCTTCTGCATGATATCTTTGAACAA 311B GAGGGCATCCC 176 GAGGGCAUCCCU 219 UAUGUAAAGGGA 262  8B AAAGTCCCAAGTGTACAAAAAGTCCC TTTACATA UUACAUA UGCCCUC GAAAGGCGTTCGCAAACCACTGACCT AGATGGAGGGAATTGTGAGGAGCAG AGGGCACCCTCTTATAAAATGCCTGT ACTTCGGTGCAGGGTTTGGTGGTGTC GGCGGTTTGGAGGCCCTTTAAGCTTC CTAACTCCTTGTCACTGGTGGATGGT GGGGTGCCGGCAGGAGGGCATCCCT TTACATAGGGGCTCATTG SiRNA# TLR7-1 MetaEnhancer_ GGGGAATGAGAAACAAAAGACAAG 154 502A GGCTCAAGGTA 177 GGCUCAAGGUA 220 UUUGCAGAUACC 263  10 502_+ GTTAATTATGACACCGGGGCTTTACA TCTGCAAA UCUGCAAA UUGAGCC ATGCTAAAAATATCCTATATACAAAG GGATATGTAGGCTGTGTTCTTTTTCCA TGTCATTACAAAGAACAGGCTCAAGG TATCTGCAAATTTCTAATAAAAATATT ATTACTTGAAAAATG SiRNA# CD38 MetaEnhancer_ GTCCACTTTTAGGAGTGTATGTACTT 155 1694A AGCATTCTGTGC 178 AGCAUUCUGUGC 221 UAAAUGAGCACAG 264  17A 1694_+ GGACACCTAAAAAATATGCTGCCACA TCATTTA UCAUUUA AAUGCU SiRNA# AGAACATTTGTTGTAGCATTctgTGCT 1694B GAGTGTATGTA 179 GAGUGUAUGUA 222 UGUCCAAGUACA 265  17B CATTTATACAGGTCTAGTTAAGTAAA CTTGGACA CUUGGACA UACACUC CTCTAGCATACTA SiRNA# CCR1 MetaEnhancer_ GCCTTTGAAAGTCTCGCATCTGCTGTT 156 258A GAGTGTTTCTCA 180 GAGUGUUUCUC 223 UAGAGUGUGAGA 266  23A 258_− TTTCAGGTCTCCAAGTCCATTCTTTGT CACTCTA ACACUCUA AACACUC SiRNA# GTTTGGACTGGTGAGTGTTTCTCACA 258B GGAGGTATCTCT 181 GGAGGUAUCUC 224 UUCUUGAAGAGA 23B CTCTATAATCGCAAAGTAGGGAGGTA TCAAGAA UUCAAGAA UACCUCC 267  TCTCTTCAAGAAGACAAGTGTCATTC AAATATTTCTGCATAACAAACCAGAC AAAACTTA SiRNA# TLR7-2 MetaEnhancer_ AGACTATTTATGCATGCATTGGTCTTT 157 341A GAGGCACCATC 182 GAGGCACCAUCA 225 UUAUGAAUGAUG 268  24A 341_− GAGCTGTTCCGCCTGCTGTCTTGTAA ATTCATAA UUCAUAA GUGCCUC SiRNA# ACTCAGAAGCAGTTTTCCTGAGGTGG 341B CTCACCATCTGA 183 CUCACCAUCUGA 226 AUGAGUCUCAGA 269  24B GTATTACTGACCATCTAGCTCACCATC GACTCAT GACUCAU UGGUGAG TGAGACTCATAAGTAGATTTGTGAGT GGTGAGGTGTAGTGAAGACCACTTG TTTGGGATTCAACATACATGCCAGCC AATGAAAATGTTAACTCACATCTGCA TATGCCTTCATCTTGTTATGGAACTGG AGGCACCATCATTCATAATGCTTAAA AATAAAACACCTGCA siRNA# WDFY1 MetaEnhancer GTTAGGTTACATATCAAGTTAGGTTC 158 512A GGCTTTAGTCCA 184 GGCUUUAGUCCA 227 UUAAGUUUGGAC 270  28A 512_− ACTGTGTACTGAAAAACCTTTAGGCC AACTTAA AACUUAA UAAAGCC SiRNA# AAAATTAAAATATGTACAACGGAGGC 512B GCCATAATTGTA 185 GCCAUAAUUGUA 228 UGACUGAUACAA 271  28B TTTAGTCCAAACTTAATTTAACAGTAC TCAGTCA UCAGUCA UUAUGGC SiRNA# TACAATTAAGTATCAGTATTGCCATA 512C TAGGTTCACTGT 186 UAGGUUCACUG 229 UCAGUACACAGU 272  28C ATGTATCAGTCAGGGT GTACTGA UGUACUGA GAACCUA GCTTGGACCCACAGTACAGATCACCC SiRNA# TNFSF MetaEnhancer_ ATCTTGGGCCTATCACACTGAGCAAT 159 734A CACACTGAGCA 187 CACACUGAGCAA 230 UCAGCAAUUGCUC 273  30 10-2 734_− TGCTGACCTGCATCTCTGTGGAGTGG ATTGCTGA UUGCUGA AGUGUG AGCCCCCAGGAGACAAGTAAAAGAC CCCCAGCCACAAC siRNA# IFNb1 MetaEnhancer_ TTCTTCTGGCTGCCTGGAAGATGCCT 160 1571A CTGTCTACATCC 188 CUGUCUACAUCC 231 UAUCCCAGGAUG 274  34A 1571_+ CTGTTATTTTAGTGAAAACATTTAGCT TGGGATA UGGGAUA UAGACAG SiRNA# CCTCGAAAGGTAGAGAGAACCAAGA 34B GGTAAAGTGTGCCATTGTAGACAGCT GGTGTGTGTGCCAGGTAGCAGTGCTT 1571B TAAAGTGTGCC 189 UAAAGUGUGCCA 232 UCUACAAUGGCAC 275  CTGTCTACATCCTGGGATATT ATTGTAGA UUGUAGA ACUUUA SiRNA# IFI16 MetaEnhancer_ TTTCTGCTATCTAGATCTTTGACTACC 161 1136A CTTATATTGTTG 190 CUUAUAUUGUU 233 UUGGGUACAACA 276  35A 1136_+ AACCAGCCAGGAGTGGTCTGCCTCTT TACCCAA GUACCCAA AUAUAAG SiRNA# CTTTGGTCTGAGCTTGCCTTGTGCTTA 1136B CTATCTAGATCT 191 CUAUCUAGAUCU 234 UAGUCAAAGAUC 277  35B TATTGTTGTACCCAAGCGAGT TTGACTA UUGACUA UAGAUAG SiRNA# PARP14 MetaEnhancer_ CGCGACCGTTCCATTCTTGAGTTTCTT 162 2972A CAACTTCTCTTG 192 CAACUUCUCUUG 235 UACAGAACAAGAG 278  36A 2972_− CACTTTGCCAGCTTGGGTGTCTCTCCC TTCTGTA UUCUGUA AAGUUG siRNA# GAGGCCGTCGTTCTAGTTATGGCTCA 2972B CTCTTGTTCTGT 193 CUCUUGUUCUG 236 AAAUGCUACAGAA 279  36B TCCAGCTGACGCTGCAACTTCTCTTGT AGCATTT UAGCAUUU CAAGAG SiRNA# TCTGTAGCATTTCTTCTACTTCTCTTTC 2972C CCGTTCCATTCT 194 CCGUUCCAUUCU 237 AAACUCAAGAAUG 280  36C TCTACCAGCTGTGTCAACCGGCT TGAGTTT UGAGUUU GAACGG SiRNA# CD38 MetaEnhancer_ CACATCTCACCCCCAGACCTGCCATT 163 3795A GAGGGTCTTTG 195 GAGGGUCUUUG 238 UGAGCUGUCAAA 281  37A 3795_− GGCATGCACATCTTTAACCACAAACC ACAGCTCA ACAGCUCA GACCCUC SiRNA# ACGATTGAAAATGAGAAAGAAAACT 3795B CTGCCATTGGCA 196 CUGCCAUUGGCA 239 AUGUGCAUGCCA 282  37B CTCCTCTAGCTGGGCGCTTCATAGGA TGCACAT UGCACAU AUGGCAG siRNA# CTAGCCAGGTACGACCATCTCTGAGG 3795C GCATGCACATCT GCAUGCACAUCU UGGUUAAAGAUG 283  37C GTCTTTGACAGCTCAGTTTTACTGCAT TTAACCA 197 UUAACCA 240 UGCAUGC AATCTGTTTTCAAGACCCTTTAAAAG ACCAGAT SiRNA# TNFSF MetaEnhancer_ CATAACTACCAGAAGCCATTGGTGGC 164 2005A CTGATTATCTCG 198 CUGAUUAUCUC 241 AUGCAGACGAGA 284  38A 10-3 2005_+ AAGATCTCAATCAGGACATGTCGGTA TCTGCAT GUCUGCAU UAAUCAG SiRNA# CAATGCTCTGATTATCTCGTCTGCATC 2005B CTGCATCCCTGA 199 CUGCAUCCCUGA 242 UAAGUAAUCAGG 285  38B CCTGATTACTTATGGTCCAGATATAA TTACTTA UUACUUA GAUGCAG SiRNA# ACTACT 2005C TACTTATGGTCC 200 UACUUAUGGUC 243 UAUAUCUGGACC 286  38C AGATATA CAGAUAUA AUAAGUA SiRNA# SAMD9 MetaEnhancer_ GTCCTTAAGGCTGATGTGAATCTCTG 165 3039A GAATCTCTGCCC 201 GAAUCUCUGCCC 244 UUGGAAAGGGCA 287  41A 3039_+ CCCTTTCCAATGTGTCATGTGATTGCT TTTCCAA UUUCCAA GAGAUUC siRNA# CCAAATTAAAACACCTATTATTATTAT 3039B TCCAATGTGTCA 202 UCCAAUGUGUCA 245 AAUCACAUGACAC 288  41B TTTG TGTGATT UGUGAUU AUUGGA SiRNA# KIAA040 MetaEnhancer_ CACCTCACTTCTGTTTTCTGTCCATTA 166 1115A CAATTAAACTCC 203 CAAUUAAACUCC 246 AGAUUUAGGAGU 289  42A 1115_+ ATGCTTCCTGCCCACGTTGTGGGGAG TAAATCT UAAAUCU UUAAUUG SiRNA# GAGCTCTCTGAACCTCTGCTGCTTCTG 1115B CTGAGGGATTC 204 CUGAGGGAUUC 247 AUAUUCUUGAAU 290  42B AGGGATTCAAGAATATATTTTTTGCT AAGAATAT AAGAAUAU CCCUCAG SiRNA# CAATTAAACTCCTAAATCTAATTTGTC 1115C CTGAACCTCTGC 205 CUGAACCUCUGC 248 AGAAGCAGCAGAG 291  42C TAAAGCTTTTCTT TGCTTCT UGCUUCU GUUCAG SiRNA# PARP9 etaEnhancer_ ACTTCCTGTCCGCGACCGTTCCATTCT 167 2972A CAACTTCTCTTG 206 CAACUUCUCUUG 249 UACAGAACAAGAG 292  43A 2972_− TGAGTTTCTTCACTTTGCCAGCTTGGG TTCTGTA UUCUGUA AAGUUG SiRNA# TGTCTCTCCCGAGGCCGTCGTTCTAG 2972B CCGTTCCATTCT 207 CCGUUCCAUUCU 250 AAACUCAAGAAUG 293  43B TTATGGCTCATCCAGCTGACGCTGCA TGAGTTT UGAGUUU GAACGG ACTTCTCTTGTTCTGTAGCATTTCTTCT ACTTCTCTTTCTCTACCAGCTGTGTCA ACCGGCTTTG SiRNA# ZBP1 MetaEnhancer_ TGATTACCTCACTCTCATGCAGGGCT 168 1228A CCGACAGAATG 208 CCGACAGAAUGC 251 UGUUUCAGCAUU 294  46A 1228_+ GAATATTACTGTTTCCCCTGTTAAACA CTGAAACA UGAAACA CUGUCGG SiRNA# AGGGTGTATTACTTCCGAAATCTGAC 1228B GGGTGTATTACT 209 GGGUGUAUUAC 252 UUUCGGAAGUAA 295  46A AACCCCAAGCACCAAAAGGTTTAAAA TCCGAAA UUCCGAAA UACACCC SiRNA# ATATCTCGAGATTGTAAAGCCTCCGA 1228C CTCATGCAGGG 210 CUCAUGCAGGGC AUAUUCAGCCCUG 46A CAGAATGCTGAAACAGGATTGCACA CTGAATAT UGAAUAU 253 CAUGAG 296  GTTGACCAGGAGCTTCTGAGGTTGTG GCGGACCCTCCATGTTTCTGACTGCC GGACAGTCACAGCCCCCTCTTCCCTA ATGCCACCAGATGTTCCCTGGGACAC CTGCC SiRNA# MNDA MetaEnhancer_ TTTCTGCTATCTAGATCTTTGACTACC 169 1136A CTTATATTGTTG 211 CUUAUAUUGUU 254 UUGGGUACAACA 297  47& & 1136_+ AACCAGCCAGGAGTGGTCTGCCTCTT TACCCAA GUACCCAA AUAUAAG 48A ACKR1 CTTTGGTCTGAGCTTGCCTTGTGCTTA 1136B CTATCTAGATCT 212 CUAUCUAGAUCU 255 UAGUCAAAGAUC 298  SiRNA# TATTGTTGTACCCAAGCGAGT TTGACTA UUGACUA UAGAUAG 47& 48B

TABLE S6 siRNAs targeting eRNA of control EP pairs. siRNA Sequence siRNA target SEQ ID siRNA sequence SEQ ID (Sense) SEQ ID (Antisense) SEQ ID name gene Items eRNA region NO: name Position NO: 5′ to 3′ NO: 5′ to 3′ NO: siRNA HLA- MetaEnhancer_ ACAGTCTACAAAGAGGCCGTGGAAGCTGT 299 475A CACCTGAT 315 CACCUGA 353 UGACGAC 391 # DMA 475_+ CGGGGAAGGAGAATGTTCAAGTAGCACAG GTTAGTC UGUUAGU UAACAUC 1A GCAATCAAACACTTCCTATTGCTCCAGGTG GTCA CGUCA AGGUG SiRNA CCAAAGCAGGAATGAAAACCTGTCCCCTCT 475B CTCTTCTT 316 CUCUUCU 354 UAGGAGU 392 #1B GTTGAATACTCTTCTTCTTCACTCCTAAAA CTTCACTC UCUUCAC GAAGAAG CTACACACCTGATGTTAGTCGTCAGCCCTC CTA UCCUA AAGAG TTCTTATCACTCTACACCTGCTGCTCTGGA GAACTCATCCAGGCCTGTGGCTCCCTGCAC GTCTACACTAGTAACCTCTGAATCCACGGT CTCCAGCACTCCCTCCTGCTCCCATCCCCA GGTGGCAGTCAGGT SiRNA HLA- MetaEnhancer_ GAATTCAAAGGGTCTCTTCTAGAGGATCCT 300 157A CTTTCTAA 317 CUUUCUA 355 AAACAUU 393 #2&3 DRA & 157_− GGGTTATGTCCTCCACAGGAACTTTGGTGT CTCCAATG ACUCCAA GGAGUUA A DRB5 TGGCCCCTCTTCCTCAAATGTGAGGATGTA TTT UGUUU GAAAG SiRNA CCAATGGCCTCCCCATTATCTCCTTTCTTT 157B GTATGTA 318 GUAUGUA 356 UGUCAGA 394 #2&3 TTCTTTCTAACTCCAATGTTTATAAAGCCT GGTTCTCT GGUUCUC GAACCUAC B ATATCCCTGTAGTGTATGTAGGTTCTCTGA GACA UGACA AUAC siRNA CAGAAGTTATACTTAGTGCTCTGTCTTTCT 157C CCTCAAAT 319 CCUCAAA 357 UACAUCC 395 #2&3 TATGGGGAAAAATCCCTGGAACTGAAGCTA GTGAGGA UGUGAGG UCACAUU C AGATCTTTAGTACTTGGAGTCACCCTACAG TGTA AUGUA UGAGG ATA SiRNA ZFAND MetaEnhancer_ ATGGTTTGTTTTCCCCTCTCCCTGCTAGAA 301 246A CTCTGAGT 320 CUCUGAG 358 AAUUGCU 396 # 6 246_+ GCACAAGGGGATTTTTCTCTGATAATCATT CTCCAGC UCUCCAG GGAGACU 6A GTGAGAACCTGTTAGAACTCCTGGAGGTAA AATT CAAUU CAGAG SiRNA AACTCAAAAGTATGGCGGCCCCCCTGAATG 246B GTGAGAA 321 GUGAGAA 359 AGUUCUA 397 # AGTCTTCCTGGAATTAACTGTCAAACTTGC CCTGTTAG CCUGUUA ACAGGUU 6B CACTCTGAGTCTCCAGCAATTCTTGAATTA AACT GAACU CUCAC CAATTCAGATTTTCCTATCCTGGTACAGGT TCCTGT siRNA PELI1 MetaEnhancer_ TACCAATGTCTCTGGGCCTTGCTCTACTAG 302 327A CTGTAACT 322 CUGUAAC 360 UAGCGAA 398 # 327_+ TACAACAGAGGAGAGAGAAATTCTAGAAGA CTGGTTC UCUGGUU CCAGAGU 9A TTTTCAACTCCCCTCCTGCTCTGTAACTCT GCTA CGCUA UACAG siRNA GGTTCGCTATGTGCTAAATGCACCTTGAAA 327B GAGAGAA 323 GAGAGAA 361 AUCUUCU 399 #9B TAAACACTTCCTTTGTGTGTGTGTGTTGCG ATTCTAGA AUUCUAG AGAAUUU CGGTGGAATCCTCACTTTACAGAAGAGGA AGAT AAGAU CUCUC siRNA APOBE MetaEnhancer_ CACTTGCTTCTAGGCTGAGGAGGGCGGGG 303 600A TTGTCAG 324 UUGUCAG 362 UGAUUCU 400 #11& C3D-1 600_+ CTGTTGTCAGAGCCCAGAATCAAAGCCAG AGCCCAG AGCCCAGA GGGCUCU 12A & AGGAGCAGGTGGACGCTGAGACTGTCCCC AATCA AUCA GACAA siRNA APOBE TCACCCTGCTCCACGGGCAATGTTGAAGT 600B GCTCCAC 325 GCUCCAC 363 UCAACAU 401 #11& C3B GGGCATCTGGGTGTT GGGCAAT GGGCAAU UGCCCGU 12B GTTGA GUUGA GGAGC siRNA DMXL1- MetaEnhancer_ ACCATGACTCACCCTCTTTCCTCGTCACCTG 304 699A CTAACTCC 326 CUAACUCC 364 AAAGAAU 402 # 1 699_+ CTAGTCCTCCCATTCACTCCCCTTCAGTCAT CTCAATTC CUCAAUU UGAGGGA 13A ATTGGCCTTGCTTCTCTTCAGACGGGCCAG TTT CUUU GUUAG siRNA CCACACTCAGGGCCTTTGCACTGACTATTC 699B CTCGTCAC 327 CUCGUCA 365 AGGACUA 403 #13B CTTCTGCCTGGAATGTTCCTCCTCCAAGTA CTGCTAGT CCUGCUA GCAGGUG TCCATATGGCTAACTCCCTCAATTCTTTGA CCT GUCCU ACGAG GATCTTTAACCACAAGGCGCTTTCCCAAAT AAGTCTTCTCTGGCTACCCTTTTTAAAATT TTAACCCCCACCCTTCACATTTTATATACT CCCCTTCCTTGCCTTTTTTCAGCTTCTTGTC siRNA ZCCHC2 MetaEnhancer_ CAATCGCTGCCTGAGTACCTATGTGTTCGT 305 804A GTGTTCGT 328 GUGUUCG 366 UAAAUCA 404 # 804_+ GGCTTGATTTACCTTATCTGTAATTCCTGGA GGCTTGA UGGCUUG AGCCACGA 14A TGTTAAAAGGACACCAAAAATCTCTGACAC TTTA AUUUA ACAC siRNA CCTGATTAGCCTACCTTGAAGAACCCAAGC 804B TTCAGAA 329 UUCAGAA 367 UAGCUCA 405 # CCAGGATTTCTGCCTTTGCCTAGAAAAAGG CTTCCTGA CUUCCUG GGAAGUU 14B ACTGATTCAGAACTTCCTGAGCTACCTAGT GCTA AGCUA CUGAA siRNA ATT 804C CTGACAC 330 CUGACACC 368 AGGCUAA 406 #14C CCTGATTA CUGAUUA UCAGGGU GCCT GCCU GUCAG siRNA CD2AP MetaEnhancer_ CACAATGAGAGTTGTCCCTAGATTTCACTG 306 1529 CAGCTTTC 331 CAGCUUU 369 AUCUCUU 407 # 1529_+ GAATGTAAATAAAAGCCTTGATCATTCTCA A CTCCAAG CCUCCAAG GGAGGAA 16A CTGCTCGACAGCCACAGTTTCACTTTGTTCT AGAT AGAU AGCUG siRNA TCATGGCTCTGCCAACCCTCTGAAACTCTC 1529 GCCACAG 332 GCCACAG 370 AACAAAG 408 # AGTCACGGGGACTGTGCTCTCAGCTTTCCT B TTTCACTT UUUCACU UGAAACU 16B CCAAGAATTTCTCCACTGCCATTGCCTCCT TGTT UUGUU GUGGC siRNA GTTTTTT 1529 CTCTGCCA 333 CUCUGCC 371 UUUCAGA 409 # C ACCCTCTG AACCCUCU GGGUUGG 16C AAA GAAA CAGAG siRNA APOBE MetaEnhancer_ ATCCTCTGACTTGGGGCAGAGCTGAGGTA 307 94A CACTGTCT 334 CACUGUC 372 UAAGCAC 410 # C3D-2 94_− GACATCTGGGTGTGTCTGGGAAACCCCGG GTGTGTG UGUGUGU ACACAGAC 18A GGAAGGTTCCTTTCTGTCCTGTCACTGTCT CTTA GCUUA AGUG siRNA GTGTGTGCTTATGTGTCTGTGTGTGTCTGT 94B CTGTGTCT 335 CUGUGUC 373 UCUGGUG 411 #18B GTCTTTGCCACCAGAAGGAGTTGGGCCTGT TTGCCACC UUUGCCA GCAAAGA TTGCTCATGAGCAGCTGTCGAGGAGGCCC AGA CCAGA CACAG ACTGTGTACCACATATGCGGCTCCTGAGG SiRNA CCR1 MetaEnhancer_ GCCTTTGAAAGTCTCGCATCTGCTGTTTTTC 308 258A GAGTGTT 336 GAGUGUU 374 UAGAGUG 412 # 258_− AGGTCTCCAAGTCCATTCTTTGTGTTTGGA TCTCACAC UCUCACAC UGAGAAA 23A CTGGTGAGTGTTTCTCACACTCTATAATCG TCTA UCUA CACUC SiRNA CAAAGTAGGGAGGTATCTCTTCAAGAAGA 258B GGAGGTA 337 GGAGGUA 375 UUCUUGA 413 #23B CAAGTGTCATTCAAATATTTCTGCATAACA TCTCTTCA UCUCUUC AGAGAUA AACCAGACAAAACTTA AGAA AAGAA CCUCC siRNA DMXL1- MetaEnhancer_ CTATCTCTCTCTTTCATGGGTCAGTTTCTAT 309 454A CTCTCTCT 338 CUCUCUC 376 UGACCCA 414 # 2 454_− TTCCCTCTGTGTTTCTGTTCATTGTCTTCCT TTCATGG UUUCAUG UGAAAGA 26A GGTGGCTAACTTCTGCTTATAGTTTCTGCTC GTCA GGUCA GAGAG siRNA CCTTTTAACTTCTGTGTGCACATGACTTGGA 454B CTGTGTTT 339 CUGUGUU 377 ACAAUGA 415 # CTTGTTATGGTACTATGCTCTGTGCTGGAAA CTGTTCAT UCUGUUC ACAGAAAC 26B CGTAGCGGTGAGTAAGGCAGCCCTGACTT TGT AUUGU ACAG SiRNA CTCAGCTCTGCATAGGACCCACAGTAGGGT 454C CCCACAG 340 CCCACAGU 378 UUCCCUA 416 #26C AGGGAATAAACACACACACACACACACAC TAGGGTA AGGGUAG CCCUACU ACACACACACAGTTGTGATGTGCTATGA GGGAA GGAA GUGGG siRNA MYCBP MetaEnhancer_ AGGAACTAGCTAACATAGGTTTTGTTATCT 310 544A GATGGTA 341 GAUGGUA 379 UCAUGUA 417 # 2 544_− GCTTCGAGTGTGCTCTGTGTGCATCCACAC CCTCTTAC CCUCUUA AGAGGUA 29A CCAAGTCCCAGGCCCCAAGAGTCTGTGTG ATGA CAUGA CCAUC SiRNA GAGCTGTGTGATGGGCTGATGGTACCTCTT 544B TGCTCTGT 342 UGCUCUG 380 UGUGGAU 418 # ACATGAGGCCTTTTGGGAGATACTGAGAA GTGCATC UGUGCAU GCACACAG 29B AGCACTGACTAGGAGTTGAGGCTCCACCC CACA CCACA AGCA SiRNA CAGATTAGTCATCATCTGTGTGT 544C GGGAGAT 343 GGGAGAU 381 UGCUUUC 419 #29C ACTGAGA ACUGAGA UCAGUAU AAGCA AAGCA CUCCC siRNA SoCS1- MetaEnhancer_ TGTAATTATTTGTTTACTGTAGGCCTCCCC 311 1477 GTGTCAG 344 GUGUCAG 382 ACAGCAG 420 #33 1 1477_− TTTGATGAGGAGCCCCCTGGGAGTGTCAGG A GCTCTCTG GCUCUCU AGAGCCU CTCTCTGCTGTCCCCCCAGCACCAGCACAA CTGT GCUGU GACAC GGC siRNA SOCS1- MetaEnhancer_ TTAGTTTCAGTTCTTTGATACTTTTTTGAGA 312 810A GGGTCAA 345 GGGUCAA 383 UAAACAA 421 # 2 810_− GGCCTGAAGGTCCTTTCCTGATATAGAACT TTTCTTTG UUUCUUU AGAAAUU A39 CACGTAAACAAATAAAAGCTTCAAGTTTTA TTTA GUUUA GACCC siRNA AGACAAGAAGGGTCAATTTCTTTGTTTATC 810B GTCCTTTC 346 GUCCUUU 384 UUCUAUA 422 #39 CAAAAAACTATCTA CTGATATA CCUGAUA UCAGGAA B GAA UAGAA AGGAC SiRNA 810C CAATTTCT 347 CAAUUUC 385 UGGAUAA 423 #39C TTGTTTAT UUUGUUU ACAAAGA CCA AUCCA AAUUG SiRNA IFI35 MetaEnhancer_ CCTACACTGAAAGCCCATGGGGTTGAAGC 313 820A CAGTGTG 348 CAGUGUG 386 UUUAUCA 424 # 820_− AGGATTTGGTTCACGCTAGAACTTCTGAGA TATCTTGA UAUCUUG AGAUACA 40A GTCAGTGTGTATCTTGATAAACAGCAACAG TAAA AUAAA CACUG SiRNA AGCTTAGTCATGAGTTCCCTGTAACTGGCT 820B GAGTCAG 349 GAGUCAG 387 UCAAGAU 425 # GCTCAGAGAGTTTGCTCCCCACCTCCTGGG TGTGTATC UGUGUAU ACACACUG 40B GAGAACTTACCTGGGAAGAGGCCAATGTTT TTGA CUUGA ACUC CTATCTAAGCCTGTCCCGTCCTCTGAGTTT CCAACCTTCTAATTTCACGTTGGGAGTGCC TC SiRNA ZBP1 MetaEnhancer_ TGATTACCTCACTCTCATGCAGGGCTGAAT 314 1228 CCGACAG 350 CCGACAGA 388 UGUUUCA 426 # 1228_+ ATTACTGTTTCCCCTGTTAAACAAGGGTGT A AATGCTG AUGCUGA GCAUUCU 46A ATTACTTCCGAAATCTGACAACCCCAAGCA AAACA AACA GUCGG SiRNA CCAAAAGGTTTAAAAATATCTCGAGATTGT 1228 GGGTGTA 351 GGGUGUA 389 UUUCGGA 427 # AAAGCCTCCGACAGAATGCTGAAACAGGA B TTACTTCC UUACUUC AGUAAUA 46A TTGCACAGTTGACCAGGAGCTTCTGAGGTT GAAA CGAAA CACCC siRNA GTGGCGGACCCTCCATGTTTCTGACTGCCG 1228 CTCATGCA 352 CUCAUGC 390 AUAUUCA 428 # GACAGTCACAGCCCCCTCTTCCCTAATGCC C GGGCTGA AGGGCUG GCCCUGC 46A ACCAGATGTTCCCTGGGACACCTGCC ATAT AAUAU AUGAG

TABLE S7 eRNA and target gene expression fold changes after eRNA KD with siRNA. eRNA mRNA siRNA name target gene Enhancer ID Distance expression fold expression fold #1A siRNA HLA-DMA MetaEnhancer_475_+ 75000 0 1.423721 #1B siRNA 75000 0.540862333 0.87843 #2A siRNA HLA-DRA MetaEnhancer_157_− 26000 2.163449332 1.016281 #2B siRNA 26000 0.615600653 0.668948 #2C siRNA 26000 1.689660424 0.366013 #3A siRNA HLA-DRB5 MetaEnhancer_157_− 44000 2.163449332 0.799221 #3B siRNA 44000 0.615600653 0.628507 #3C siRNA 44000 1.689660424 0.268563 #5AsiRNA TNFSF10-1 MetaEnhancer_116_+ 69000 0.60149862 0.69573 #5BsiRNA 69000 0.684600064 0.874542 #5CsiRNA 69000 0.77916458 1.228246 #6A siRNA ZFAND6 MetaEnhancer_246_+ 34000 2.518677954 0.963707 #6B siRNA 34000 0.827405623 0.331405 #7AsiRNA IRF8 MetaEnhancer_259_+ 73000 0.707106781 0.649169 #7BsiRNA 73000 1.194687532 0.521233 #8AsiRNA MLLT6 MetaEnhancer_311_+ 50000 2.795810671 0.831238 #8BsiRNA 50000 7.193364285 2.434007 #9A siRNA PELI1 MetaEnhancer_327_+ 82000 1.713096791 2.750969 #9B siRNA 82000 0.983915733 1.018613 #10 siRNA TLR7-1 MetaEnhancer_502_+ 20000 0.631417726 2.93494473 #11A siRNA APOBEC3D-1 MetaEnhancer_600_+ 65000 1.580082624 1.701334 #11B siRNA 65000 0.763129604 1.990779 #12A siRNA APOBEC3B MetaEnhancer_600_+ 26000 1.580082624 1.239708 #12B siRNA 26000 0.381564802 0.552227 #13A siRNA DMXL1-1 MetaEnhancer_699_+ 37000 0.625320044 1.815038 #13B siRNA 37000 1.006722921 1.624505 #14AsiRNA ZCCHC2 MetaEnhancer_804_+ 15000 1.447336117 5.27791 #14BsiRNA 15000 6.573826285 6.276528 #14CsiRNA 15000 0 4.469045 #16A siRNA CD2AP MetaEnhancer_1529_+ 62000 2.417082417 1.781797 #16B siRNA 62000 0.990777721 1.749165 #16C siRNA 62000 0.692538733 1.280464 #17A siRNA CD38-1 MetaEnhancer_1694_+ 5500 0.409896999 1.04005993 #17B siRNA 5500 3.863745316 0.369249 #18A siRNA APOBEC3D-2 MetaEnhancer_94_− 65000 0.287114879 1.59479 #18B siRNA 65000 2.356588726 3.2566 #23A siRNA CCR1 MetaEnhancer_258_− 91000 2.328929014 0.604271 #23B siRNA 91000 3.49833068 0.759576 #24A siRNA TLR7-2 MetaEnhancer_341_− 22000 6.320330495 8.186991 #24B siRNA 22000 0.761368436 1.48795751 #26A siRNA DMXL1-2 MetaEnhancer_454_− 38000 0.835087919 1.35347352 #26B siRNA 38000 3.792283097 1.543993 #26C siRNA 38000 0 4.958831 #28A siRNA WDFY1 MetaEnhancer_512_− 2600 0.174742204 0.104627 #28B siRNA 2600 1.522736872 2.075319 #28C siRNA 2600 0.540862333 0.169184 #29A siRNA MYCBP2 MetaEnhancer_544_− 87000 3.023039857 0.664328 #29B siRNA 87000 4.845458993 1.119846 #29C siRNA 87000 0.422395587 0.084786 #30 siRNA TNFSF10-2 MetaEnhancer_734_− 67000 0.835087919 0.73373618 #34A siRNA IFNb1 MetaEnhancer_1571_+ 18000 0 0.502316 #34B siRNA 18000 0.410845157 0.575678 #35A siRNA IFI16 MetaEnhancer_1136_+ 2300 0.23648036 0.439317 #35B siRNA 2300 0.34268249 1.254112 #36A siRNA PARP14 MetaEnhancer_2972_− 18000 0.434280777 0.993115 #36B siRNA 18000 0.720315074 1.887792 #36C siRNA 18000 0.699001117 0.667435 #37A siRNA CD38-2 MetaEnhancer_3795_− 22000 1.032923445 1.135504 #37B siRNA 22000 0.779182582 0.562529 #37C siRNA 22000 0.240376317 0.92445 #38AsiRNA TNFSF10-3 MetaEnhancer_2005_+ 27000 0.801069878 0.279955 #38BsiRNA 27000 0.92873141 1.219762 #38CsiRNA 27000 0.930879716 0.391369 #39A siRNA SOCS1-2 MetaEnhancer_810_− 48400 1.587364376 2.244872 #39B siRNA 48400 1.498272459 3.160092 #39C siRNA 48400 1.674000548 1.286365 #40A siRNA IFI35 MetaEnhancer_820_− 77000 0.550952558 0.237062 #40B siRNA 77000 0.217637641 0.390483 #41A siRNA SAMD9 MetaEnhancer_3039_+ 62000 0.848664754 0.304244 #41B siRNA 62000 0.168007786 0.281909 #42A siRNA KIAA0040 MetaEnhancer_1115_+ 94000 0.187712939 0.554426 #42B siRNA 94000 0.295917448 0.255678 #42C siRNA 94000 0.251146313 0.425059 #43A siRNA PARP9 etaEnhancer_2972_− 96000 0.297982601 0.29937 #43B siRNA 96000 0.751059963 0.40239 #46A siRNA ZBP1 MetaEnhancer_1228_+ 120000 0.227930622 0.903335 #46B siRNA 120000 5.051341805 2.065751 #46C siRNA 120000 0.082469244 0.3423 #47A siRNA MNDA MetaEnhancer_1136_+ 156000 0.23981603 0.430276 #47B siRNA 156000 0.273573425 0.733736 #48A siRNA ACKR1 MetaEnhancer_1136_+ 196000 0.23981603 0.673617 #48B siRNA 196000 0.273573425 0.842842

RT-qPCR. was performed to check the transcription level after siRNA KD for eRNA and promoter RNA. Total RNA extract with Trizol (Invitrogen) was treated with DNaseI (Roche) for 30 min at 37° C. and further extracted with acidic phenol: chloroform and precipitated with salt, glycogen, and pure ethanol. The RNA was reverse-transcribed using ImProm-II™ (Promega) with 100 uM of oligo-dTs or random decamers. The resulting cDNA was incubated with 10 μg of RNaseH and RNase cocktail for 30 min at 37° C. and purified using the PCR purification kit (MACHEREY-NAGEL). 5˜10 ng of purified cDNA was quantified by using a FastStart Universal SYBR Green Mater Mix (Roche) on qPCR machine (Realplex2, Eppendorf in Germany). The inventor used GAPDH as the internal control. The primers of GAPDH for RT-qPCR are forward 5′-TGCACCACCAACTGCTTAGC-3′ (SEQ ID NO: 647) and reverse 5′-GGCATGGACTGTGGTCATGAG-3′ (SEQ ID NO: 648). To calculate the relative expression fold change (sample/control), he used the scrambled siRNA transfection as the negative control. The qPCR primers were designed against each siRNA-targeting region of eRNA and promoter and the sequences of primers were listed in Table S8 and Table S9.

TABLE S8  eRNA primers eRNA- eRNA- SEQ Forward Reverse target ID primer Forward primer SEQ ID primer Reverse primer SEQ ID gene enhancer ID sequence NO: ID sequence NO: ID sequence NO: HLA- MetaEnhancer_ ACAGTCTACAAAGAG 429 eRNA#1 CTTCTTCACTCCTA 460 eRNA#1 AGAGTGATAAGAA 521  DMA 475_+ GCCGTGGAAGCTGTC A-F AAACTACACACC A-R GAGGGCTGA GGGGAAGGAGAATGT eRNA#l AATGAAAACCTGT 461 eRNA#l AGGTGTGTAGTTT 522  TCAAGTAGCACAGGC B-F CCCCTCTG B-R TAGGAGTGAAGAA AATCAAACACTTCCT ATTGCTCCAGGTGCC AAAGCAGGAATGAAA ACCTGTCCCCTCTGT TGAATACTCTTCTTC TTCACTCCTAAAACT ACACACCTGATGTTA GTCGTCAGCCCTCTT CTTATCACTCTACAC CTGCTGCTCTGGAGA ACTCATCCAGGCCTG TGGCTCCCTGCACGT CTACACTAGTAACCT CTGAATCCACGGTCT CCAGCACTCCCTCCT GCTCCCATCCCCAGG TGGCAGTCAGGT HLA- MetaEnhancer_ GAATTCAAAGGGTCTC 430 eRNA#2- CTCCCCATTATCTC 462 eRNA#2- AGGGATATAGGCT 523  DRAS &  157_- TTCTAGAGGATCCTGG 3A-F CTTTCTTTT 3A-R TTATAAACATTGG DRBS GTTATGTCCTCCACAG eRNA#2- GTGTATGTAGGTT 463 eRNA#2- TTTTTCCCCATAAG 524  GAACTTTGGTGTTGGC 3B-F CTCTGACAGAAGT 3B-R AAAGACAGA CCCTCTTCCTCAAATG eRNA#2- TCCTCCACAGGAA 464 eRNA#2- GGCCATTGGTACA 525  TGAGGATGTACCAATG 3C-F CTTTGGT 3C-R TCCTCAC GCCTCCCCATTATCTC CTTTCTTTTTCTTTCT AACTCCAATGTTTATA AAGCCTATATCCCTGT AGTGTATGTAGGTTCT CTGACAGAAGTTATAC TTAGTGCTCTGTCTTT CTTATGGGGAAAAATC CCTGGAACTGAAGCTA AGATCTTTAGTACTTG GAGTCACCCTACAGAT A TNFSF MetaEnhancer_ TAAACCAGGATCTTCTT 431 eRNA#5 TTGTATGTATTGTG 465 eRNA#5 CATTTCCAGGTGA 526  10-1 116_+ CAGCCTCCAAGGTAAGG A-F AACGCCACT A-R ATAACTTTGG AAATGTGTGATCTCCAA eRNA#5 AGGATCTTCTTCAG 466 eRNA#5 AATACATACAAGA 527  GCTCCCTCTTGTATGTA BC-F CCTCCA BC-R GGGAGCTTGG TTGTGAACGCCACTGTC AGAAGAGAAACACCAAA GTTATTCACCTGGAAAT GTTGCAGTATGAAGACC ATGTATTTGATGGAGAG G ZFAN MetaEnhancer_ ATGGTTTGTTTTCCCCT 432 eRNA#6 TCTTCCTGGAATTA 467 eRNA#6 TGTAATTCAAGAAT 528  D6 246_+ CTCCCTGCTAGAAGCAC A-F ACTGTCAAA A-R TGCTGGAGAC AAGGGGATTTTTCTCTG eRNA#6 GGGATTTTTCTCTG 468 eRNA#6 TTGAGTTTTACCTC 529  ATAATCATTGTGAGAAC B-F ATAATCATTGTG B-R CAGGAGTTCT CTGTTAGAACTCCTGGA GGTAAAACTCAAAAGTA TGGCGGCCCCCCTGAAT GAGTCTTCCTGGAATTA ACTGTCAAACTTGCCAC TCTGAGTCTCCAGCAAT TCTTGAATTACAATTCA GATTTTCCTATCCTGGT ACAGGTTCCTGT IRF8 MetaEnhancer_ GGCTCAGGCTGAGAGGA 433 eRNA#7 TGAGAGGATATTC 469 eRNA#7 GAACTGACTCTCCA 530  259_+ TATTCTGCCGTTGTAGT A-F TGCCGTTG A-R GTCTTCTTAAA TTTGLTCGGGGCCATTC eRNA#7 TGGGGGACTAAGT 470 eRNA#7 CCTGCATGTGTTCT 531  GTTTTAAGAAGACTGGA B-F TCTTATCATGT B-R CAATAAGC GAGTCAGTTCCAGTTTG TCTTGGGGGACTAAGTT CTTATCATGTGGTTTCT ACTGGTGGCTTATTGAG AACACATGCAGGTACAG MLLT6 MetaEnhancer_ CCCAGCCCTCAGTGGCC 434 eRNA#8 TGGCTGTTCTTGGT 471 eRNA#8 CGGGACTTTTTGTA 532  311_+ CCACAGCAGCTTGGCTG A-F TTTGTTT A-R CACTTGG TTCTTGGTTTTGTTTCT eRNA#8 ACTCCTTGTCACTG 472 eRNA#8 GCCCCTATGTAAA 533  CTCTGCTTCTGCATGAT B-F GTGGATG B-R GGGATGC ATCTTTGAACAAAAAGT CCCAAGTGTACAAAAAG TCCCGAAAGGCGTTCGC AAACCACTGACCTAGAT GGAGGGAATTGTGAGGA GCAGAGGGCACCCTCTT ATAAAATGCCTGTACTT CGGTGCAGGGTTTGGTG GTGTCGGCGGTTTGGAG GCCCTTTAAGCTTCCTA ACTCCTTGTCACTGGTG GATGGTGGGGTGCCGGC AGGAGGGCATCCCTTTA CATAGGGGCTCATTG PELI1 MetaEnhancer_ TACCAATGTCTCTGGGC 435 eRNA#9 TTTTCAACTCCCCT 473 eRNA#9 TTTCAAGGTGCATT 534  327_+ CTTGCTCTACTAGTACA A-F CCTGCT A-R TAGCACA ACAGAGGAGAGAGAAAT eRNA#9 TCTCTGGGCCTTGC 474 eRNA#9 GCAGGAGGGGAG 535  TCTAGAAGATTTTCAAC B-F TCTACT B-R TTGAAAAT TCCCCTCCTGCTCTGTA ACTCTGGTT CGCTATGTGCTAAATG CACCTTGAAATAAACA CTTCCTTTGTGTGTGT GTGTTGCGCGGTGGAA TCCTCACTTTACAGAA GAGGA TLR7- MetaEnhancer_ GGGGAATGAGAAACAA 436 eRNA#1 AGGCTGTGTTCTTT 475 eRNA#1 AGAAATTTGCAGA 536  1 502_+ AAGACAAGGTTAATTA 0-F TTCCATGT 0-R TACCTTGAGC TGACACCGGGGCTTTA CAATGCTAAAAATATC CTATATACAAAGGGAT ATGTAGGCTGTGTTCT TTTTCCATGTCATTAC AAAGAACAGGCTCAAG GTATCTGCAAATTTCT AATAAAAATATTATTA CTTGAAAAATG APOB MetaEnhancer_ CACTTGCTTCTAGGCT 437 eRNA#1 CACTTGCTTCTAGG 476 eRNA#1 TCCTCTGGCTTTGA 537  EC3D- 600_+ GAGGAGGGCGGGGCTG 1-12A-F CTGAGGA 1-12A-R TTCTGG 1& TTGTCAGAGCCCAGAA eRNA#1 AGGTGGACGCTGA 477 eRNA#1 CCAGATGCCCACTT 538  APOB TCAAAGCCAGAGGAGC 1-12B-F GACTGT 1-12B-R CAACAT EC3B AGGTGGACGCTGAGAC TGTCCCCTCACCCTGC TCCACGGGCAATGTTG AAGTGGGCATCTGGGT GTGT DMXL MetaEnhancer ACCATGACTCACCCTC 438 eRNA#1 CTGGAATGTTCCTC 478 eRNA#1 AAGCGCCTTGTGG 539  1-1 _699_* TTTCCTCGTCACCTGC 3A-F CTCCAA 3A-R TTAAAGA TAGTCCTCCCATTCAC eRNA#1 ACCCTCTTTCCTCG 479 eRNA#1 GCAAGGCCAATAT 540  TCCCCTTCAGTCATAT 3B-F TCACCT 3B-R GACTGAA TGGCCTTGCTTCTCTT CAGACGGGCCAGCCAC ACTCAGGGCCTTTGCA CTGACTATTCCTTCTG CCTGGAATGTTCCTCC TCCAAGTATCCATATG GCTAACTCCCTCAATT CTTTGAGATCTTTAAC CACAAGGCGCTTTCCC AAATAAGTCTTCTCTG GCTACCCTTTTTAAAA TTTTAACCCCCACCCT TCACATTTTATATACT CCCCTTCCTTGCCTTT TTTCAGCTTCTTGTC ZCCHC MetaEnhancer_ CAATCGCTGCCTGAGT 439 eRNA#1 CCTATGTGTTCGTG 480 eRNA#1 TTTGGTGTCCTTTT 541  2 804_+ ACCTATGTGTTCGTGG 4A-F GCTTGA 4A-R AACATCCA CTTGATTTACCTTATC eRNA#1 AAGAACCCAAGCC 481 eRNA#1 GCTCAGGAAGTTC 542  TGTAATTCCTGGATGT 4B-F CAGGAT 4 B-R TGAATCAGTC TAAAAGGACACCAAAA eRNA#1 AAGGACACCAAAA 482 eRNA#1 ATCCTGGGCTTGG 543  ATCTCTGACACCCTG 4C-F ATCTCTGACA 4C-R GTTCTT ATTAGCCTACCTTGAA GAACCCAAGCCCAGGA TTTCTGCCTTTGCCT AGAAAAAGGACTGATT CAGAACTTCCTGAGCT ACCTAGTATT CD38 MetaEnhancer_ GTCCACTTTTAGGAGT 440 eRNA#1 GTAGCATTCTGTGC 483 eRNA#1 TAAATGAGCACAG 544  1694_ GTATGTACTTGGACAC 7A-F TCATTTATAC 7A-R AATGC CTAAAAAATATGCTG eRNA#1 CCACTTTTAGGAGT eRNA#1 CAAATGTTCTTGTG CCACAAGAACATTTGT 7B-F GTATGTACTTGG 484 7B-R GCAGCA 545  TGTAGCATTCTGTGCT CATTTATACAGGTCTA GTTAAGTAAACTCTAG CATACTA APOB MetaEnhancer_ ATCCTCTGACTTGGGG 441 eRNA#1 ATCTGGGTGTGTC 485 eRNA#1 GCACACACAGACA 546  EC3D- 94_- CAGAGCTGAGGTAGAC 8A-F TGGGAAA 8A-R GTGACAGG 2 ATCTGGGTGTGTCTGG eRNA#1 ATGAGCAGCTGTC 486 eRNA#1 ACACAGACAGTGC 547  GAAACCCCGGGGAAGG 8B-F GAGGAG 8B-R CTCAGGA TTCCTTTCTGTCCTGT CACTGTCTGTGTGTGC TTATGTGTCTGTGTGT GTCTGTGTCTTTGCCA CCAGAAGGAGTTGGGC CTGTTTGCTCATGAGC ACTGTCGAGGAGGCCC ACTGTGTCCACATATG CGGCTCCTGAGG CCR1 MetaEnhancer_ GCCTTTGAAAGTCTCG 442 eRNA#2 TCCATTCTTTGTGT 487 eRNA#2 TGCGATTATAGAG 548  258_- CATCTGCTGTTTTTCA 3A-F TTGGACTG 3A-R TGTGAGAAACA GGTCTCCAAGTCCATT eRNA#2 CGCAAAGTAGGGA 488 eRNA#2 TGCAGAAATATTT 549  CTTTGTGTTTGGACTG 3B-F GGTATCTCTT 3B-R GAATGACACTTG GTGAGTGTTTCTCACA CTCTATAATCGCAAAG TAGGGAGGTATCTCTT CAAGAAGACAAGTGTC ATTCAAATATTTCTGC ATAACAAACCAGTACA AAACTTA TLR7- MetaEnhancer_ AGACTATTTATGCATG 443 eRNA#2 TATGGAACTGGAG 489 eRNA#2 TGCAGGTGTTTTAT 550  2 341_- CATTGGTCTTTGAGCT 4A-F GCACCAT 4A-R TTTTAAGCA GTTCCGCCTGCTGTCT eRNA#2 TGACCATCTAGCTC eRNA#2 TCCCAAACAAGTG TGTAAACTCAGAAGCA 4B-F ACCATCTG 490 4B-R GTCTTCA 551  GTTTTCCTGAGGTGGG TATTACTGACCATCTA GCTCACCATCTGAGAC TCATAAGTAGATTTGT GAGTGGTGAGGTG TAGTGAAGACCACTTG TTTGGGATTCAACATA CATGGCCAGCCAATGA AAATGTTAACTCACAT CTGCATATGCCTTCAT CTTGTTATGGAACTGG AGGCACCATCATTCAT AATGCTTAAAAATAAA ACACCTGCA DMXL MetaEnhancer_ CTATCTCTCTCTTTCA 444 eRNA#2 TCTCTCTTTCATGG 491 eRNA#2 GCAGAAGTTAGCC 552  1-2 454_- TGGGTCAGTTTCTATT 6AB-F GTCAGTTTC 6AB-R ACCAGGA TCCCTCTGTGTTTCTG eRNA#2 CAGCCCTGACTTCT 492 eRNA#2 CAACTGTGTGTGT 553  TTCATTGTCTTCCTGG 6C-F CAGCTC 6C-R GTGTGTGTG TGGCTAACTTCTGCTT ATAGTTTCTGCTCCCT TTTAACTTCTGTGTGC ACATGACTTGGACTTG TTATGGTACTATGCTC TG TGCTGGAAACGTAGCG GTGAGTAAGGCAGCCC TGACTTCTCAGCTCTG CATAGGACCCACAGTA GGGTAGGGAATAAACA CACACACACACACACA CACACACACACAGTTG TGATGTGCTATGA WDFY MetaEnhancer_ GTTAGGTTACATATCA 445 eRNA#2 GGCCAAAATTAAA 493 eRNA#2 ACTGTTAAATTAAG 554  1 512_- AGTTAGGTTCACTGTG 8A-F ATATGTACAACG 8A-R TTTGGACTAAAGC TACTGAAAAACCTTTA eRNA#2 CAACGGAGGCTTT 494 eRNA#2 GACTGATACAATT 555  GGCCAAAATTAAAATA 8B-F AGTCCAA 8B-R ATGGCAATACTGA TGTACAACGGAGGCTT eRNA#2 GGTTACATATCAA 495 eRNA#2 TTTTGGCCTAAAG 556  TAGTCCAAACTTAATT 8C-F GTTAGGTTCACTG 8C-R GTTTTTA TAACAGTACTACAATT AAGTATCAGTATTGCC ATAATTGTATCAGTCA GGGT MYCB MetaEnhancer_ AGGAACTAGCTAACAT 446 eRNA#2 CTGTGTGGAGCTG 496 eRNA#2 CTCCCAAAAGGCC 557  P2 544_- AGGTTTTGTTATCTGC 9A-F TGTGATG 9A-R TCATGTA TTCGAGTGTGCTCTGT eRNA#2 CTGCTTCGAGTGT 497 eRNA#2 TCACACAGCTCCAC 558  GTGCATCCACACCCAA 9B-F GCTCTGT 9B-R ACAGACT GTCCCAGGCCCCAAGA eRNA#2 GGCCTTTTGGGAG 498 eRNA#2 GGTTGGAGCCTCA 559  GTCTGTGTGGAGCTGT 9C-F ATACTGA 9C-R ACTCCTA GTGATGGGCTGATGGT ACCTCTTACATGAGGC CTTTTGGGAGATACTG AGAAAGCACTGGACTA GGAGTTGAGGCTCCAA CCCCAGATTAGCATCA TCTGTGTGT TNFSF MetaEnhancer_ GCTTGGACCCACAGTA 447 eRNA#3 CCATCTTGGGCCTA 499 eRNA#3 CTCCACAGAGATG 560  10-2 734_- CAGATCACCCATCTTG 0-F TCACAC 0-R CAGGTCA GGCCTATCACACTGAG CAATTGCTGACCTGCA TCTCTGTGGAGTGGAG CCCCCAGGAGACAAGT AAAAGACCCCCAGCCA CAAC IFNb1 MetaEnhancer_ TTCTTCTGGCTGCCTG 448 eRNA#3 TTTAGCTCCTCGAA 500 eRNA#3 TTTAGCTCCTCGAA 561  1571_ GAAGATGCCTCTGTTA 4A-F AGGTAGAGA 4A-R AGGTAGAGA TTTTAGTGAAAACATT eRNA#3 GCCTGGAAGATGC 501 eRNAB#3 CTACCTGGCACAC 562  TAGCTCCTCGAAAGGT 4B-F CTCTGTT 48-R ACACCAG AGAGAGAACCAAGAGG TAAAGTGTGCCATTGT AGACAGCTGGTGTGTG TGCCAGGTAGCAGTGC TTCTGTCTACATCCTG GGATATT IFI16 MetaEnhancer_ TTTCTGCTATCTAGAT 449 eRNA#3 CTGCTATCTAGATC 502 eRNA#3 CTCGCTTGGGTAC 563  1136_ CTTTGACTACCAACCA 5-F TTTG 5-R AACAAT GCCAGGAGTGGTCTGC CTCTTCTTTGGTCTGA GCTTGCCTTGTGCTTA TATTGTTGTACCCAAG CGAGT PARP14 MetaEnhancer_ CGCGACCGTTCCATTC 450 eRNA#3 CGACCGTTCCATTC 503 eRNA#3 AGAGAAGTTGCAG 564  2972_- TTGAGTTTCTTCACTT 6AB-F TTGAGT 6AB-R CGTCAGC TGCCAGCTTGGGTGTC eRNA#3 CGACCGTTCCATTC 504 eRNA#3 AGAGAAGTTGCAG 565  TCTCCCGAGGCCGTCG 6C-F TTGAGT 6C-R CGTCAGC TTCTAGTTATGGCTCA TCCAGCTGACGCTGC AACTTCTCTTGTTCTG TAGCATTTCTTCTACT TCTCTTTCTCTACCAG CTGTGTCAACCGGCT CD38 MetaEnhancer_ CACATCTCACCCCCAG 451 eRNA#3 TGGGCGCTTCATA 505 eRNA#3 TCTGGTCTTTTAAA 566  3795_- ACCTGCCATTGGCATG 7A-F GGACT 7A-R GGGTCTTGA CACATCTTTAACCACA eRNA#3 ACATCTCACCCCCA 506 eRNA#3 CTATGAAGCGCCC 567  AACCACGATTGAAAAT 7BC-F GACCT 7BC-R AGCTAGA GAGAAAGAAAACTCTC CTCTAGCTGGGCGC TTCATAGGACTAGCCA GGTACGACCATCTCTG AGGGTCTTTGACAGCT CAGTTTTACTGCATAA TCTGTTTTCAAGACCC TTTAAAAGACCAGAT TNFSF MetaEnhancer_ CATAACTACCAGAAGC 452 eRNA#3 TGGTGGCAAGATC 507 eRNA#3 TCAGGGATGCAGA 568  10-3 2005_ CATTGGTGGCAAGATC 8AB-F TCAATCA 8AB-R CGAGATA TCAATCAGGACATGTC eRNA#3 CGGTACAATGCTCT 508 eRNA#3 GGACCATAAGTAA 569  GGTACAATGCTCTGAT 8C-F GATTATCTCG 8C-R TCAGGGATGC TATCTCGTCTGCATCC CTGATTACTTATGGTC CAGATATAAACTACT SOCS1 MetaEnhancer_ TTAGTTTCAGTT 453 eRNA#3 TCACGTAAACAAA 509 eRNA#3 CAAAGAAATTGAC 570  810_- CTTTGATACTTT 9AC-F TAAAAGCTTCA 9AC-R CCTTCTTGTC TTTGAGAGGCCT eRNA#3 TTTTTGAGAGGCCT 510 eRNA#3 TGAAGCTTTTATTT 571  GAAGGTCCTTTC 9B-F GAAGGT 9B-R GTTTACGTGAG CTGATATAGAAC TCACGTAAACAA ATAAAAGCTTCA AGTTTTAAGACA AGAAGGGTCAAT TTCTTTGTTTAT CCAAAAAACTAT CTA IFI35 MetaEnhancer_ CCTACACTGAAAG 454 eRNA#4 ATGGGGTTGAAGC 511 eRNA#4 CAGCCAGTTACAG 572  820_- CCCATGGGGTTGA 0-F AGGATTT 0-R GGAACTCA AGCAGGATTTGGT TCACGCTAGAACT TCTGAGAGTCAGT GTGTATCTTGATA AACAGCAACAGAG CTTAGTCATGAGT TCCCTGTAACTGG CTGCTCAGAGAGT TTGCTCCCCACCT CCTGGGGAGAACT TACCTGGGAAGAG GCCAATGTTTCTA TCTAAGCCTGTCC CGTCCTCTGAGTT TCCAACCTTCTAA TTTCACGTTGGG AGTGCCTC SAMD MetaEnhancer_ GTCCTTAAGGCTG 455 eRNA#4 AAGGCTGATGTGA 512 eRNA#4 TGGAGCAATCACA 573  9 3039_ ATGTGAATCTCTG 1-F ATCTCTGC 1-R TGACACA CCCTTTCCAATGT GTCATGTGATTGC TCCAAATTAAAAC ACCTATTATTATT ATTTTG KIAA0 MetaEnhancer_ CACCTCACTTCTG 456 eRNA#4 TCTGCTGCTTCTGA 513 eRNA#4 GATTTAGGAGTTT 574  40 1115_ TTTTCTGTCCATT 2A-F GGGATT 2A-R AATTGAGCAAAAA AATGCTTCCTGCC eRNA#4 CCACGTTGTGGGG 514 eRNA#4 GAATCCCTCAGAA 575  CACGTTGTGGGGA 2BC-F AGGAG 2BC-R GCAGCAG GGAGCTCTCTGAA CCTCTGCTGCTTC TGAGGGATTCAAG AATATATTT PARP9 MetaEnhancer_ ACTTCCTGTCCGC 457 eRNA#4 GGCCGTCGTTCTA 515 eRNA#4 CCGGTTGACACAG 576  2972_- GACCGTTCCATTC 3A-F GTTATGG 3A-R CTGGTAG TTGAGTTTCTTCA eRNA#4 CGACCGTTCCATTC 516 eRNA#4 TCAGCTGGATGAG 577  CTTTGCCAGCTTG 38-F TTGAGT 3B-R CCATAACT GGTGTCTCTCCCG AGGCCGTCGTTCT AGTTATGGCTCAT CCAGCTGACGCTG CAACTTCTCTTGT TCTGTAGCATTTC TTCTACTTCTCTT TCTCTACCAGCTG TGTCAACCGGCT TTG ZBP1 MetaEnhancer_ TGATTACCTCAC 458 eRNA#4 ACCAAAAGGTTTA 517 eRNA#4 ACCTCAGAAGCTC 578  1228_ TCTCATGCAGGG 6A-F AAAATATCTCG 6A-R CTGGTCA CTGAATATTACT eRNA#4 CACTCTCATGCAG 518 eRNA#4 GTGCTTGGGGTTG 579  GTTTCCCCTGTT 68C-F GGCTGA 6BC-R TCAGATT AAACAAGGGTGT ATTACTTCCGAA ATCTGACAACCC CAAGCACCAAAA GGTTTAAAAATA TCTCGAGATTGT AAAGCCTCCGAC AGAATGCTGAAA CAGGATTGCACA GTTGACCAGGAG CTTCTGAGGTTG TGGCGGACCCTC CATGTTTCTGAC TGCCGGACAGTC ACAGCCCCCTCT TCCCTAATGCCA CCAGATGTTCCC TGGGACACCTGC C MNDA MetaEnhancer_ TTTCTGCTATCT 459 eRNA#4 CAGGAGTGGTCTG 519 eRNA#4 ACTCGCTTGGGTA 580  & 1136_ AGATCTTTGACT 7-48A-F CaCTTC 7-48A-R CAACAAT ACKR1 ACCAACCAGCCA eRNA#4 TGCTATCTAGATCT 520 eRNA#4 GAAGAGGCAGACC 581  GGAGTGGTCTGC 7-48B-F TTGACTACCAACC 7-48B-R ACTCCTG CTCTTCTTTGGT CTGAGCTTGCCT TGTGCTTATATT GTTGTACCCAAG CGAGT

TABLE S9 mRNA primers  SEQ SEQ Gene Forward ID Reverse ID name primer NO: primer NO: HLA-DMA GATCTAAG 582 GCAGCTCC 613 GCCACCCT TTGGTTCT CTCG GTTC HLA-DRA TCCCGAGC 583 TGATAGCC 614 TCTACTGA CATGATTC CTCC CTGA HLA-DRB5 CCAGCATG 584 AGCCAGTG 615 GTGTGTCT GGGAGCTC GAAG AG TNFSF10 AAGGAAGG 585 GACTGCAG 616 GCTTCAGT GAGCACTG GACC TGAA ZFAND6 CCAATCCA 586 CCTCCGTC 617 GTGGCTCT CGCTGTTT CCT ATTA IRF8 TCGACACC 587 CTCTTCCC 618 AGCCAGTT AGCCTCTT CTTC CTGC MLLT6 AGCTCATG 588 AGTAGACC 619 GGAGTATG AGCGGGTT AAGGA CTCG PELI1 CCCTCCTT 589 CCGCTGCT 620 GCGAGTGT GCTAGTGG ATGT AG TLR7 TCCCATCA 590 ATGATTGT 621 GAGGCTCA CTGTGGCC TGGA AGGG APOBEC3D AACTTGGC 591 GAGTTCGA 622 TCACTGCA GACCAGCC ACCT TGAC APOBEC3B TGCTGGGA 592 CCATCCTT 623 CACCTTTG CAGTTTCC TGTA CTGA DMXL1 GTGTCCGT 593 CCACGGAG 624 TGCAGGAC AAGCAGTG TAGG GT ZCCHC2 CCTGAGGG 594 AACTTGCA 625 AACACTTG CGGCTCTA GAGA CCTC CD2AP GCGCTGAA 595 GCTCCTCC 626 GAGACTGG TCCTCCTC TAGG CTC CD38 GGGAGGTG 596 CGAGGATC 627 CAGTTTCA AGGACCAG GAAC GATA CCR1 CATCTCCA 597 CACACAGT 628 ACCAAGGA GGGCACAT CCCC TTTGT SEMA4D AACACTCA 598 CGTCTGGA 629 CCGTGAAG GTCTGTCC GTCTG CTTC WDFY1 GGCCGAAA 599 CTCCTTGG 630 TCCACTCC GGATGAGC AG AG MYC8P2 GAAGGAGG 600 ACACACAG 631 TCGCTGTC CCCTTTTC TTTG CAAC SOCS1 CTGGAGCA 601 AGGGGAAG 632 CTACGTGG GAGCTCAG CG GTAG IFNB1 TCTCCTAG 602 GCCATCAG 633 CCTGTGCC TCACTTAA TCTG ACAGCA IFI16 GAATAGGA 603 AAGTTCCC 634 GCAAGCCA AGAAACGG GCAC AACC PARP14 TACTTCCA 604 CGGGTAGA 635 GAGCCCGA AGAACACC AGAG AGGA CD38 GGGAGGTG 605 CGAGGATC 636 CAGTTTCA AGGACCAG GAAC GATA IFI35 AGGGATTT 606 AAGGGCTG 637 CACGGAAA TGGTCTCT TGAA CTCA SAMD9 CCGTTAAA 607 TGTGGGGA 638 ACCAGAAT AAACCATC GAGGA TCTT KIAA0040 TTCAGGAA 608 TGTGTTCC 639 GTTGTGCC CTGCCTTC TGTG CTAC PARP9 CTGCCCTT 609 CGAAGGAA 640 TCACTGAA GCTGGAGA CTCC GCTA ZBP1 GCATCTAT 610 CTGCAAGG 641 TTCCGGGC AGTCGGAG TGTA AGAC MNDA TGGCTCTA 611 CACTGTCC 642 ACAAGTGC GTAAAGCT CATT TTGGA ACKR1 CTGTCCCA 612 CTGTCGAG 643 TTGTCCCC GCTGCATA TAGA ATGA

Apoptosis assay. To evaluate the cell viability, the inventor performed Western-Blot with cleaved caspase-3 antibody (Cell Signaling technology, #9661) and Annexin-V apoptosis detection flow cytometry assay as described (Goodwin et al., 2017). Virus was infected at 36 hours after siRNA transfection as described in previous method section (targeting TNFSF10 eRNAs and IFNB1 eRNA, L2), and cells (300,000 per well) were harvested at 24 hours, 72 hours, and 96 hours after virus infection with cold PBS wash. For the negative control experiment, 5 uM of TIC10 (SML1068, Sigma-Aldrich) was treated for 48 hrs to activate the apoptosis pathway by inducing the level of TNFSF10 expression.

Western blot. In order to extract protein from each well, 40 ul of RIPA buffer with freshly made proteinase inhibitor cocktail (Roche) was added to cell pellet. 12% SDS gel was run for 1 hour with constant voltage (120V), followed by transfer to a membrane (Immun-Blot PVDF membrane sandwiches, BioRad) with constant 0.1 A for 45 min. The size of cleaved caspase-3 is 17-19 kDa. β-Actin (45 kDa) was used as an internal standard.

Flow cytometry. Cell death was measured using the PE Annexin-V Apoptosis Detection Kit I (BD Pharmingen) according to the manufacturer's instruction. Cells were collected and stained with annexin-V and 7-AAD and analyzed by flow cytometry (SH800, Sony) and FlowJo software.

Data accession. Time-course GRO-seq and ChIP-seq data have been uploaded to the Array Express (world-wide-web at ebi.ac.uk/arrayexpress/) with the accession numbers E-MTAB-6047 and E-MTAB-6050, respectively.

All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the disclosure. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the disclosure as defined by the appended claims.

F. REFERENCES

The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference.

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What is claimed is:
 1. A method of inhibiting a TNFSF10 gene expression in a human cell comprising contacting the human cell with a single-stranded antisense compound comprising a sequence selected from SEQ ID NOs: 170, 171, 172, 213, 214, 215, 187, 230, 198, 199, 200, 241, 242, or 243, thereby inhibiting expression of the TNFSF10 gene in the human cell.
 2. The method of claim 1, wherein the eRNA transcription is initiated from an RNA polymerase II (PolII) binding site and is capable of elongating bidirectionally.
 3. The method of claim 1, wherein the eRNA transcription is initiated from an RNA polymerase II (PolII) binding site and is capable of elongating unidirectionally.
 4. The method of claim 2, wherein the eRNA is capable of enhancing transcription of the TNFSF10 gene.
 5. The method of claim 1, wherein the transcriptional start site of the TNFSF10 gene is located on a chromosome at least about 1 kilobase (kb) from the genomic enhancer sequence or region.
 6. The method of claim 1, wherein the human cell is an epithelium cell, a hematopoietic cell, a monocyte, a macrophage, a fibroblast cell, a neuron, a breast cell, or a cancer cell.
 7. The method of claim 6, wherein the human cell contacted with the antisense compound is in a subject.
 8. The method of claim 3, wherein the eRNA is capable of enhancing transcription of the TNFSF10 gene. 